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add Gupta23 - 10.1172/JCI166032, resolve #880 (#897)
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* add Gupta23 - 10.1172/JCI166032, resolve #880

* Fix Gupta23

* update variant consensus

* update variant consensus

* Autogenerated data updated by HIVDB Bot

---------

Co-authored-by: HIVDB Bot <[email protected]>
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@KaimingTao @hivdb-bot
KaimingTao and hivdb-bot authored May 2, 2023
1 parent 7a48234 commit 95c4b05
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Showing 11 changed files with 260 additions and 0 deletions.
1 change: 1 addition & 0 deletions tables/articles.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -773,3 +773,4 @@ Cheung23,10.1002/jmv.28694,NULL,"Cheung, AKL",2023,2023-04-26,NULL
Yamasoba23,10.1101/2023.04.06.535883,NULL,"Yamasoba, D",2023,2023-04-26,NULL
Focosi22,10.1016/j.jcvp.2022.100097,NULL,"Focosi, D",2022,2023-05-01,NULL
Jary22,10.3390/v14020226,NULL,"Jary, A",2022,2023-05-01,NULL
Gupta23,10.1172/JCI166032,NULL,"Gupta, A",2023,2023-05-01,NULL
142 changes: 142 additions & 0 deletions tables/isolate_mutations.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,50 @@ B.1.1.7 Spike,S,681,H,NULL,NULL
B.1.1.7 Spike,S,716,I,NULL,NULL
B.1.1.7 Spike,S,982,A,NULL,NULL
B.1.1.7 Spike,S,1118,H,NULL,NULL
B.1.1.7 Spike+S:484A,S,69,del,NULL,NULL
B.1.1.7 Spike+S:484A,S,70,del,NULL,NULL
B.1.1.7 Spike+S:484A,S,144,del,NULL,NULL
B.1.1.7 Spike+S:484A,S,484,A,NULL,NULL
B.1.1.7 Spike+S:484A,S,501,Y,NULL,NULL
B.1.1.7 Spike+S:484A,S,570,D,NULL,NULL
B.1.1.7 Spike+S:484A,S,614,G,NULL,NULL
B.1.1.7 Spike+S:484A,S,681,H,NULL,NULL
B.1.1.7 Spike+S:484A,S,716,I,NULL,NULL
B.1.1.7 Spike+S:484A,S,982,A,NULL,NULL
B.1.1.7 Spike+S:484A,S,1118,H,NULL,NULL
B.1.1.7 Spike+S:484D,S,69,del,NULL,NULL
B.1.1.7 Spike+S:484D,S,70,del,NULL,NULL
B.1.1.7 Spike+S:484D,S,144,del,NULL,NULL
B.1.1.7 Spike+S:484D,S,484,D,NULL,NULL
B.1.1.7 Spike+S:484D,S,501,Y,NULL,NULL
B.1.1.7 Spike+S:484D,S,570,D,NULL,NULL
B.1.1.7 Spike+S:484D,S,614,G,NULL,NULL
B.1.1.7 Spike+S:484D,S,681,H,NULL,NULL
B.1.1.7 Spike+S:484D,S,716,I,NULL,NULL
B.1.1.7 Spike+S:484D,S,982,A,NULL,NULL
B.1.1.7 Spike+S:484D,S,1118,H,NULL,NULL
B.1.1.7 Spike+S:493R,S,69,del,NULL,NULL
B.1.1.7 Spike+S:493R,S,70,del,NULL,NULL
B.1.1.7 Spike+S:493R,S,144,del,NULL,NULL
B.1.1.7 Spike+S:493R,S,493,R,NULL,NULL
B.1.1.7 Spike+S:493R,S,501,Y,NULL,NULL
B.1.1.7 Spike+S:493R,S,570,D,NULL,NULL
B.1.1.7 Spike+S:493R,S,614,G,NULL,NULL
B.1.1.7 Spike+S:493R,S,681,H,NULL,NULL
B.1.1.7 Spike+S:493R,S,716,I,NULL,NULL
B.1.1.7 Spike+S:493R,S,982,A,NULL,NULL
B.1.1.7 Spike+S:493R,S,1118,H,NULL,NULL
B.1.1.7 Spike+S:493K,S,69,del,NULL,NULL
B.1.1.7 Spike+S:493K,S,70,del,NULL,NULL
B.1.1.7 Spike+S:493K,S,144,del,NULL,NULL
B.1.1.7 Spike+S:493K,S,493,K,NULL,NULL
B.1.1.7 Spike+S:493K,S,501,Y,NULL,NULL
B.1.1.7 Spike+S:493K,S,570,D,NULL,NULL
B.1.1.7 Spike+S:493K,S,614,G,NULL,NULL
B.1.1.7 Spike+S:493K,S,681,H,NULL,NULL
B.1.1.7 Spike+S:493K,S,716,I,NULL,NULL
B.1.1.7 Spike+S:493K,S,982,A,NULL,NULL
B.1.1.7 Spike+S:493K,S,1118,H,NULL,NULL
S:69del+70del+141del+501Y+570D+614G+681H+716I+982A,S,69,del,NULL,NULL
S:69del+70del+141del+501Y+570D+614G+681H+716I+982A,S,70,del,NULL,NULL
S:69del+70del+141del+501Y+570D+614G+681H+716I+982A,S,141,del,NULL,NULL
Expand Down Expand Up @@ -9734,6 +9778,104 @@ BA.1 Spike,S,856,K,NULL,NULL
BA.1 Spike,S,954,H,NULL,NULL
BA.1 Spike,S,969,K,NULL,NULL
BA.1 Spike,S,981,F,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,67,V,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,69,del,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,70,del,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,95,I,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,142,D,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,143,del,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,144,del,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,145,del,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,211,I,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,212,del,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,214,ins,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,339,D,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,417,N,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,440,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,446,S,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,477,N,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,478,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,484,A,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,493,R,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,496,S,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,498,R,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,501,Y,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,505,H,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,547,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,614,G,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,655,Y,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,679,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,681,H,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,764,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,796,Y,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,856,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,954,H,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,969,K,NULL,NULL
BA.1 Spike:-371L-373P-375F,S,981,F,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,67,V,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,69,del,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,70,del,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,95,I,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,142,D,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,143,del,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,144,del,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,145,del,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,211,I,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,212,del,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,214,ins,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,417,N,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,440,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,446,S,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,477,N,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,478,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,484,A,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,493,R,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,496,S,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,498,R,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,501,Y,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,505,H,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,547,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,614,G,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,655,Y,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,679,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,681,H,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,764,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,796,Y,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,856,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,954,H,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,969,K,NULL,NULL
BA.1 Spike:-339D-371L-373P-375F,S,981,F,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,67,V,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,69,del,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,70,del,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,95,I,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,142,D,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,143,del,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,144,del,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,145,del,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,211,I,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,212,del,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,214,ins,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,446,S,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,477,N,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,478,K,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,484,A,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,493,R,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,496,S,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,498,R,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,501,Y,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,505,H,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,547,K,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,614,G,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,655,Y,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,679,K,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,681,H,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,764,K,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,796,Y,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,856,K,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,954,H,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,969,K,NULL,NULL
BA.1 Spike:-339D-373P-375F-417N-440K,S,981,F,NULL,NULL
BA.1 Spike:493K,S,67,V,NULL,NULL
BA.1 Spike:493K,S,69,del,NULL,NULL
BA.1 Spike:493K,S,70,del,NULL,NULL
Expand Down
7 changes: 7 additions & 0 deletions tables/isolates.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,10 @@ S:69del+70del+144del+494P+501Y+570D+614G+681H+716I+982A+1118H,Alpha/S494P,FALSE,
S:69del+70del+144del+490S+501Y+570D+614G+681H+716I+982A+1118H,Alpha/F490S,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike:-144del+145del,Alpha,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:484K,Alpha/E484K,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:484A,Alpha/E484A,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:484D,Alpha/E484D,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:493R,Alpha/Q493R,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:493K,Alpha/Q493K,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:494P,Alpha/S494P,FALSE,NULL,NULL,NULL,TRUE
B.1.1.7 Spike+S:484K+494P,Alpha/E484K+S494P,FALSE,NULL,NULL,NULL,TRUE
hCoV-19/France/ARA-isl136/2020,Alpha,FALSE,1707039,NULL,NULL,TRUE
Expand Down Expand Up @@ -1171,6 +1175,9 @@ BA.1 Spike:+K356T,Omicron/BA.1/K356T,FALSE,NULL,NULL,NULL,TRUE
BA.1 Spike:+R493Q,Omicron/BA.1/R493Q,FALSE,NULL,NULL,NULL,TRUE
S:67V+69del+70del+95I+142D+143del+144del+145del+211I+212del+214EPEins+339D+371L+373P+375F+417N+440K+446S+477N+478K+484A+493R+496S+498R+501Y+505H+547K+614G+655Y+679K+681H+764K+796Y+856K+954H+969K+981F,Omicron/BA.1,FALSE,NULL,NULL,NULL,TRUE
BA.1 Spike:Q493K,Omicron/BA.1,FALSE,NULL,NULL,NULL,TRUE
BA.1 Spike:-371L-373P-375F,Omicron/BA.1/-371L/-373P/-375F,FALSE,NULL,NULL,NULL,TRUE
BA.1 Spike:-339D-371L-373P-375F,Omicron/BA.1/-339D/-371L/-373P/-375F,FALSE,NULL,NULL,NULL,TRUE
BA.1 Spike:-339D-373P-375F-417N-440K,Omicron/BA.1/-339D/-373P/-375F/-417N/-440K,FALSE,NULL,NULL,NULL,TRUE
S:67V+69del+70del+95I+142D+143del+144del+145del+211I+212del+214EPEins+417N+496S+498R+501Y+547K+614G+655Y+679K+681H+764K+796Y+856K+954H+969K+981F,Omicron/BA.1,FALSE,NULL,NULL,NULL,TRUE
S:67V+69del+70del+95I+142D+143del+144del+145del+211I+212del+214EPEins+440K+446S+496S+498R+547K+614G+655Y+679K+681H+764K+796Y+856K+954H+969K+981F,Omicron/BA.1,FALSE,NULL,NULL,NULL,TRUE
S:67V+69del+70del+95I+142D+143del+144del+145del+211I+212del+214EPEins+339D+371L+373P+375F+417N+440K+446S+477N+478K+484A+493R+496S+498R+501Y+505H+547K+614G+655Y+679K+681H+701V+764K+796Y+856K+954H+969K+981F,Omicron/BA.1,FALSE,NULL,NULL,NULL,TRUE
Expand Down
5 changes: 5 additions & 0 deletions tables/rx_antibodies/gupta23-mab.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
ref_name,rx_name,ab_name
Gupta23,Bamlanivimab,Bamlanivimab
Gupta23,Bamlanivimab+Etesevimab,Bamlanivimab
Gupta23,Bamlanivimab+Etesevimab,Etesevimab
Gupta23,Sotrovimab,Sotrovimab
18 changes: 18 additions & 0 deletions tables/subject_infections/gupta23-inf.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
ref_name,subject_name,infection_date_cmp,infection_date,infected_var_name,location,immune_status,severity,section
Gupta23,Pt_1,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_2,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_3,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_4,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_5,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_6,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_7,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_8,~,2021-03-01,Alpha,Italy,NULL,Mild,NULL
Gupta23,Pt_9,~,2021-12-01,Omicron/BA.1,Italy,NULL,Mild,NULL
Gupta23,Pt_10,~,2021-12-01,Omicron/BA.1.1,Italy,NULL,Mild,NULL
Gupta23,Pt_11,~,2021-12-01,Omicron/BA.1.1,Italy,NULL,Mild,NULL
Gupta23,Pt_12,~,2021-12-01,Omicron/BA.1,Italy,NULL,Mild,NULL
Gupta23,Pt_13,~,2021-12-01,Omicron/BA.1,Italy,NULL,Mild,NULL
Gupta23,Pt_14,~,2021-12-01,Omicron/BA.1,Italy,NULL,Mild,NULL
Gupta23,Pt_15,~,2021-12-01,Omicron/BA.1,Italy,NULL,Mild,NULL
Gupta23,Pt_16,~,2021-12-01,Omicron/BA.1,Italy,NULL,Mild,NULL
Gupta23,Pt_17,~,2021-12-01,Omicron/BA.1.1,Italy,NULL,Mild,NULL
35 changes: 35 additions & 0 deletions tables/subject_isolates/gupta23-sbjiso.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
ref_name,subject_name,collection_date_cmp,collection_date,iso_name,iso_source,iso_culture,location,section
Gupta23,Pt_1,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_2,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_3,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_4,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_5,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_6,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_7,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_8,~,2021-03-01,B.1.1.7 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_9,~,2021-12-01,BA.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_10,~,2021-12-01,BA.1.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_11,~,2021-12-01,BA.1.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_12,~,2021-12-01,BA.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_13,~,2021-12-01,BA.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_14,~,2021-12-01,BA.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_15,~,2021-12-01,BA.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_16,~,2021-12-01,BA.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_17,~,2021-12-01,BA.1.1 Spike,NP,FALSE,Italy,NULL
Gupta23,Pt_1,~,2021-03-08,B.1.1.7 Spike+S:484A,NP,FALSE,Italy,NULL
Gupta23,Pt_2,~,2021-03-08,B.1.1.7 Spike+S:493R,NP,FALSE,Italy,NULL
Gupta23,Pt_3,~,2021-03-08,B.1.1.7 Spike+S:494P,NP,FALSE,Italy,NULL
Gupta23,Pt_4,~,2021-03-08,B.1.1.7 Spike+S:484K,NP,FALSE,Italy,NULL
Gupta23,Pt_5,~,2021-03-08,B.1.1.7 Spike+S:484K,NP,FALSE,Italy,NULL
Gupta23,Pt_6,~,2021-03-08,B.1.1.7 Spike+S:493K,NP,FALSE,Italy,NULL
Gupta23,Pt_7,~,2021-03-08,B.1.1.7 Spike+S:484D,NP,FALSE,Italy,NULL
Gupta23,Pt_8,~,2021-03-08,B.1.1.7 Spike+S:493R,NP,FALSE,Italy,NULL
Gupta23,Pt_9,~,2021-12-08,BA.1 Spike:+E340K,NP,FALSE,Italy,NULL
Gupta23,Pt_10,~,2021-12-08,BA.1 Spike:-371L-373P-375F,NP,FALSE,Italy,NULL
Gupta23,Pt_11,~,2021-12-08,BA.1 Spike:-339D-371L-373P-375F,NP,FALSE,Italy,NULL
Gupta23,Pt_12,~,2021-12-08,BA.1 Spike:+E340D,NP,FALSE,Italy,NULL
Gupta23,Pt_13,~,2021-12-08,BA.1 Spike:+E340D,NP,FALSE,Italy,NULL
Gupta23,Pt_14,~,2021-12-08,BA.1 Spike:+E340K,NP,FALSE,Italy,NULL
Gupta23,Pt_15,~,2021-12-08,BA.1 Spike:+E340V,NP,FALSE,Italy,NULL
Gupta23,Pt_16,~,2021-12-08,BA.1 Spike:+E340D,NP,FALSE,Italy,NULL
Gupta23,Pt_17,~,2021-12-08,BA.1 Spike:-339D-373P-375F-417N-440K,NP,FALSE,Italy,NULL
18 changes: 18 additions & 0 deletions tables/subject_treatments/gupta23-prx.csv
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@@ -0,0 +1,18 @@
ref_name,subject_name,rx_name,start_date_cmp,start_date,end_date_cmp,end_date,dosage,dosage_unit,section
Gupta23,Pt_1,Bamlanivimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_2,Bamlanivimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_3,Bamlanivimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_4,Bamlanivimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_5,Bamlanivimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_6,Bamlanivimab+Etesevimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_7,Bamlanivimab+Etesevimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_8,Bamlanivimab+Etesevimab,~,2021-03-01,~,2021-03-01,NULL,NULL,NULL
Gupta23,Pt_9,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_10,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_11,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_12,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_13,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_14,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_15,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_16,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
Gupta23,Pt_17,Sotrovimab,~,2021-12-01,~,2021-12-01,NULL,NULL,NULL
10 changes: 10 additions & 0 deletions tables/subject_vaccines/gupta23-vacc.csv
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ref_name,subject_name,vaccination_date_cmp,vaccination_date,vaccine_name,dosage,location,section
Gupta23,Pt_9,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_10,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_11,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_12,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_13,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_14,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_15,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_16,~,2021-06-01,Unknown vaccine,2,Italy,NULL
Gupta23,Pt_17,~,2021-06-01,Unknown vaccine,2,Italy,NULL
17 changes: 17 additions & 0 deletions tables/subjects.csv
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Expand Up @@ -1847,6 +1847,23 @@ Gruell22b,CP,Human,NULL,20
Gruell22b,VP,Human,NULL,30
Gruell22c,BNT162b2_3dose,Human,NULL,30
Guigon21,Patient,Human,1958,1
Gupta23,Pt_1,Human,NULL,1
Gupta23,Pt_10,Human,NULL,1
Gupta23,Pt_11,Human,NULL,1
Gupta23,Pt_12,Human,NULL,1
Gupta23,Pt_13,Human,NULL,1
Gupta23,Pt_14,Human,NULL,1
Gupta23,Pt_15,Human,NULL,1
Gupta23,Pt_16,Human,NULL,1
Gupta23,Pt_17,Human,NULL,1
Gupta23,Pt_2,Human,NULL,1
Gupta23,Pt_3,Human,NULL,1
Gupta23,Pt_4,Human,NULL,1
Gupta23,Pt_5,Human,NULL,1
Gupta23,Pt_6,Human,NULL,1
Gupta23,Pt_7,Human,NULL,1
Gupta23,Pt_8,Human,NULL,1
Gupta23,Pt_9,Human,NULL,1
Gushchin21,S003,Human,1986,1
Gushchin21,S004,Human,1991,1
Gushchin21,S005,Human,1981,1
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3 changes: 3 additions & 0 deletions tables/treatments.csv
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Expand Up @@ -5817,6 +5817,9 @@ Guo23,WRAIR-2057
Guo23,ION_300
Guo23,COVOX-45
Guo23,N-612-056
Gupta23,Bamlanivimab
Gupta23,Bamlanivimab+Etesevimab
Gupta23,Sotrovimab
Hao22,mAb_206
Hao22,mAb_234
Hao22,mAb_297
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4 changes: 4 additions & 0 deletions tables/variants.csv
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Expand Up @@ -195,6 +195,7 @@ Alpha/A475V+E484K,FALSE,TRUE
Alpha/D138Y+A701V,FALSE,TRUE
Alpha/E484A,FALSE,TRUE
Alpha/E484K,FALSE,TRUE
Alpha/E484D,FALSE,FALSE
Alpha/E484K+S494P,FALSE,FALSE
Alpha/E484K+Q493R+S494P,FALSE,TRUE
Alpha/E484Q,FALSE,TRUE
Expand Down Expand Up @@ -442,6 +443,9 @@ Omicron/BA.1/D405N,FALSE,TRUE
Omicron/BA.1/R408S,FALSE,TRUE
Omicron/BA.1/-Q493R,FALSE,TRUE
Omicron/BA.1/-G446S/-Q493R,FALSE,TRUE
Omicron/BA.1/-371L/-373P/-375F,FALSE,FALSE
Omicron/BA.1/-339D/-371L/-373P/-375F,FALSE,FALSE
Omicron/BA.1/-339D/-373P/-375F/-417N/-440K,FALSE,FALSE
Omicron/BA.2/-Q493R,FALSE,TRUE
Omicron/XAF,FALSE,TRUE
Omicron/BA.2.75/K356T,FALSE,TRUE
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