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Fix FDA24 (#1050)
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* Fix FDA24

* fix JD.1.1 Spike

* fix XBB.1.5.1 Spike

* update FDA24

* update FDA24

* update FDA24

* update FDA24
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@KaimingTao
KaimingTao authored Jul 19, 2024
1 parent 761e823 commit ea91a03
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Showing 6 changed files with 372 additions and 21 deletions.
282 changes: 282 additions & 0 deletions tables/isolate_mutations.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25290,6 +25290,49 @@ XBB.1.5.10 Spike,S,764,K,NULL,NULL
XBB.1.5.10 Spike,S,796,Y,NULL,NULL
XBB.1.5.10 Spike,S,954,H,NULL,NULL
XBB.1.5.10 Spike,S,969,K,NULL,NULL
XBB.1.5.1 Spike,S,19,I,NULL,NULL
XBB.1.5.1 Spike,S,24,S,NULL,NULL
XBB.1.5.1 Spike,S,25,del,NULL,NULL
XBB.1.5.1 Spike,S,26,del,NULL,NULL
XBB.1.5.1 Spike,S,27,del,NULL,NULL
XBB.1.5.1 Spike,S,83,A,NULL,NULL
XBB.1.5.1 Spike,S,142,D,NULL,NULL
XBB.1.5.1 Spike,S,144,del,NULL,NULL
XBB.1.5.1 Spike,S,146,Q,NULL,NULL
XBB.1.5.1 Spike,S,183,E,NULL,NULL
XBB.1.5.1 Spike,S,213,E,NULL,NULL
XBB.1.5.1 Spike,S,252,V,NULL,NULL
XBB.1.5.1 Spike,S,339,H,NULL,NULL
XBB.1.5.1 Spike,S,346,T,NULL,NULL
XBB.1.5.1 Spike,S,368,I,NULL,NULL
XBB.1.5.1 Spike,S,371,F,NULL,NULL
XBB.1.5.1 Spike,S,373,P,NULL,NULL
XBB.1.5.1 Spike,S,375,F,NULL,NULL
XBB.1.5.1 Spike,S,376,A,NULL,NULL
XBB.1.5.1 Spike,S,405,N,NULL,NULL
XBB.1.5.1 Spike,S,408,S,NULL,NULL
XBB.1.5.1 Spike,S,417,N,NULL,NULL
XBB.1.5.1 Spike,S,440,K,NULL,NULL
XBB.1.5.1 Spike,S,445,P,NULL,NULL
XBB.1.5.1 Spike,S,446,S,NULL,NULL
XBB.1.5.1 Spike,S,460,K,NULL,NULL
XBB.1.5.1 Spike,S,477,N,NULL,NULL
XBB.1.5.1 Spike,S,478,K,NULL,NULL
XBB.1.5.1 Spike,S,484,A,NULL,NULL
XBB.1.5.1 Spike,S,486,P,NULL,NULL
XBB.1.5.1 Spike,S,490,S,NULL,NULL
XBB.1.5.1 Spike,S,498,R,NULL,NULL
XBB.1.5.1 Spike,S,501,Y,NULL,NULL
XBB.1.5.1 Spike,S,505,H,NULL,NULL
XBB.1.5.1 Spike,S,573,I,NULL,NULL
XBB.1.5.1 Spike,S,614,G,NULL,NULL
XBB.1.5.1 Spike,S,655,Y,NULL,NULL
XBB.1.5.1 Spike,S,679,K,NULL,NULL
XBB.1.5.1 Spike,S,681,H,NULL,NULL
XBB.1.5.1 Spike,S,764,K,NULL,NULL
XBB.1.5.1 Spike,S,796,Y,NULL,NULL
XBB.1.5.1 Spike,S,954,H,NULL,NULL
XBB.1.5.1 Spike,S,969,K,NULL,NULL
XBB.1.5 Spike:K478R+F456L+H505Y,S,19,I,NULL,NULL
XBB.1.5 Spike:K478R+F456L+H505Y,S,24,S,NULL,NULL
XBB.1.5 Spike:K478R+F456L+H505Y,S,25,del,NULL,NULL
Expand Down Expand Up @@ -25808,3 +25851,242 @@ HV.1 Spike,S,764,K,NULL,NULL
HV.1 Spike,S,796,Y,NULL,NULL
HV.1 Spike,S,954,H,NULL,NULL
HV.1 Spike,S,969,K,NULL,NULL
XBB.2.3 Spike,S,19,I,NULL,NULL
XBB.2.3 Spike,S,24,S,NULL,NULL
XBB.2.3 Spike,S,25,del,NULL,NULL
XBB.2.3 Spike,S,26,del,NULL,NULL
XBB.2.3 Spike,S,27,del,NULL,NULL
XBB.2.3 Spike,S,83,A,NULL,NULL
XBB.2.3 Spike,S,142,D,NULL,NULL
XBB.2.3 Spike,S,144,del,NULL,NULL
XBB.2.3 Spike,S,146,Q,NULL,NULL
XBB.2.3 Spike,S,183,E,NULL,NULL
XBB.2.3 Spike,S,213,E,NULL,NULL
XBB.2.3 Spike,S,253,G,NULL,NULL
XBB.2.3 Spike,S,339,H,NULL,NULL
XBB.2.3 Spike,S,346,T,NULL,NULL
XBB.2.3 Spike,S,368,I,NULL,NULL
XBB.2.3 Spike,S,371,F,NULL,NULL
XBB.2.3 Spike,S,373,P,NULL,NULL
XBB.2.3 Spike,S,375,F,NULL,NULL
XBB.2.3 Spike,S,376,A,NULL,NULL
XBB.2.3 Spike,S,405,N,NULL,NULL
XBB.2.3 Spike,S,408,S,NULL,NULL
XBB.2.3 Spike,S,417,N,NULL,NULL
XBB.2.3 Spike,S,440,K,NULL,NULL
XBB.2.3 Spike,S,445,P,NULL,NULL
XBB.2.3 Spike,S,446,S,NULL,NULL
XBB.2.3 Spike,S,460,K,NULL,NULL
XBB.2.3 Spike,S,477,N,NULL,NULL
XBB.2.3 Spike,S,478,K,NULL,NULL
XBB.2.3 Spike,S,484,A,NULL,NULL
XBB.2.3 Spike,S,486,P,NULL,NULL
XBB.2.3 Spike,S,490,S,NULL,NULL
XBB.2.3 Spike,S,498,R,NULL,NULL
XBB.2.3 Spike,S,501,Y,NULL,NULL
XBB.2.3 Spike,S,505,H,NULL,NULL
XBB.2.3 Spike,S,521,S,NULL,NULL
XBB.2.3 Spike,S,614,G,NULL,NULL
XBB.2.3 Spike,S,655,Y,NULL,NULL
XBB.2.3 Spike,S,679,K,NULL,NULL
XBB.2.3 Spike,S,681,H,NULL,NULL
XBB.2.3 Spike,S,764,K,NULL,NULL
XBB.2.3 Spike,S,796,Y,NULL,NULL
XBB.2.3 Spike,S,954,H,NULL,NULL
XBB.2.3 Spike,S,969,K,NULL,NULL
EU.1.1 Spike,S,19,I,NULL,NULL
EU.1.1 Spike,S,24,S,NULL,NULL
EU.1.1 Spike,S,25,del,NULL,NULL
EU.1.1 Spike,S,26,del,NULL,NULL
EU.1.1 Spike,S,27,del,NULL,NULL
EU.1.1 Spike,S,83,A,NULL,NULL
EU.1.1 Spike,S,142,D,NULL,NULL
EU.1.1 Spike,S,144,del,NULL,NULL
EU.1.1 Spike,S,146,Q,NULL,NULL
EU.1.1 Spike,S,183,E,NULL,NULL
EU.1.1 Spike,S,213,E,NULL,NULL
EU.1.1 Spike,S,252,V,NULL,NULL
EU.1.1 Spike,S,339,H,NULL,NULL
EU.1.1 Spike,S,346,T,NULL,NULL
EU.1.1 Spike,S,368,I,NULL,NULL
EU.1.1 Spike,S,371,F,NULL,NULL
EU.1.1 Spike,S,373,P,NULL,NULL
EU.1.1 Spike,S,375,F,NULL,NULL
EU.1.1 Spike,S,376,A,NULL,NULL
EU.1.1 Spike,S,405,N,NULL,NULL
EU.1.1 Spike,S,408,S,NULL,NULL
EU.1.1 Spike,S,410,V,NULL,NULL
EU.1.1 Spike,S,417,N,NULL,NULL
EU.1.1 Spike,S,440,K,NULL,NULL
EU.1.1 Spike,S,445,P,NULL,NULL
EU.1.1 Spike,S,446,S,NULL,NULL
EU.1.1 Spike,S,460,K,NULL,NULL
EU.1.1 Spike,S,477,N,NULL,NULL
EU.1.1 Spike,S,478,K,NULL,NULL
EU.1.1 Spike,S,484,A,NULL,NULL
EU.1.1 Spike,S,486,P,NULL,NULL
EU.1.1 Spike,S,490,S,NULL,NULL
EU.1.1 Spike,S,498,R,NULL,NULL
EU.1.1 Spike,S,501,Y,NULL,NULL
EU.1.1 Spike,S,505,H,NULL,NULL
EU.1.1 Spike,S,521,S,NULL,NULL
EU.1.1 Spike,S,614,G,NULL,NULL
EU.1.1 Spike,S,655,Y,NULL,NULL
EU.1.1 Spike,S,679,K,NULL,NULL
EU.1.1 Spike,S,681,H,NULL,NULL
EU.1.1 Spike,S,764,K,NULL,NULL
EU.1.1 Spike,S,796,Y,NULL,NULL
EU.1.1 Spike,S,954,H,NULL,NULL
EU.1.1 Spike,S,969,K,NULL,NULL
HK.3 Spike,S,19,I,NULL,NULL
HK.3 Spike,S,24,S,NULL,NULL
HK.3 Spike,S,25,del,NULL,NULL
HK.3 Spike,S,26,del,NULL,NULL
HK.3 Spike,S,27,del,NULL,NULL
HK.3 Spike,S,52,H,NULL,NULL
HK.3 Spike,S,83,A,NULL,NULL
HK.3 Spike,S,142,D,NULL,NULL
HK.3 Spike,S,144,del,NULL,NULL
HK.3 Spike,S,146,Q,NULL,NULL
HK.3 Spike,S,183,E,NULL,NULL
HK.3 Spike,S,213,E,NULL,NULL
HK.3 Spike,S,252,V,NULL,NULL
HK.3 Spike,S,339,H,NULL,NULL
HK.3 Spike,S,346,T,NULL,NULL
HK.3 Spike,S,368,I,NULL,NULL
HK.3 Spike,S,371,F,NULL,NULL
HK.3 Spike,S,373,P,NULL,NULL
HK.3 Spike,S,375,F,NULL,NULL
HK.3 Spike,S,376,A,NULL,NULL
HK.3 Spike,S,405,N,NULL,NULL
HK.3 Spike,S,408,S,NULL,NULL
HK.3 Spike,S,417,N,NULL,NULL
HK.3 Spike,S,440,K,NULL,NULL
HK.3 Spike,S,445,P,NULL,NULL
HK.3 Spike,S,446,S,NULL,NULL
HK.3 Spike,S,455,F,NULL,NULL
HK.3 Spike,S,456,L,NULL,NULL
HK.3 Spike,S,460,K,NULL,NULL
HK.3 Spike,S,477,N,NULL,NULL
HK.3 Spike,S,478,K,NULL,NULL
HK.3 Spike,S,484,A,NULL,NULL
HK.3 Spike,S,486,P,NULL,NULL
HK.3 Spike,S,490,S,NULL,NULL
HK.3 Spike,S,498,R,NULL,NULL
HK.3 Spike,S,501,Y,NULL,NULL
HK.3 Spike,S,505,H,NULL,NULL
HK.3 Spike,S,614,G,NULL,NULL
HK.3 Spike,S,655,Y,NULL,NULL
HK.3 Spike,S,679,K,NULL,NULL
HK.3 Spike,S,681,H,NULL,NULL
HK.3 Spike,S,764,K,NULL,NULL
HK.3 Spike,S,796,Y,NULL,NULL
HK.3 Spike,S,954,H,NULL,NULL
HK.3 Spike,S,969,K,NULL,NULL
JD.1.1 Spike,S,19,I,NULL,NULL
JD.1.1 Spike,S,24,S,NULL,NULL
JD.1.1 Spike,S,25,del,NULL,NULL
JD.1.1 Spike,S,26,del,NULL,NULL
JD.1.1 Spike,S,27,del,NULL,NULL
JD.1.1 Spike,S,83,A,NULL,NULL
JD.1.1 Spike,S,142,D,NULL,NULL
JD.1.1 Spike,S,144,del,NULL,NULL
JD.1.1 Spike,S,146,Q,NULL,NULL
JD.1.1 Spike,S,183,E,NULL,NULL
JD.1.1 Spike,S,213,E,NULL,NULL
JD.1.1 Spike,S,252,V,NULL,NULL
JD.1.1 Spike,S,339,H,NULL,NULL
JD.1.1 Spike,S,346,T,NULL,NULL
JD.1.1 Spike,S,368,I,NULL,NULL
JD.1.1 Spike,S,371,F,NULL,NULL
JD.1.1 Spike,S,373,P,NULL,NULL
JD.1.1 Spike,S,375,F,NULL,NULL
JD.1.1 Spike,S,376,A,NULL,NULL
JD.1.1 Spike,S,405,N,NULL,NULL
JD.1.1 Spike,S,408,S,NULL,NULL
JD.1.1 Spike,S,417,N,NULL,NULL
JD.1.1 Spike,S,440,K,NULL,NULL
JD.1.1 Spike,S,445,P,NULL,NULL
JD.1.1 Spike,S,446,S,NULL,NULL
JD.1.1 Spike,S,455,F,NULL,NULL
JD.1.1 Spike,S,456,L,NULL,NULL
JD.1.1 Spike,S,460,K,NULL,NULL
JD.1.1 Spike,S,475,V,NULL,NULL
JD.1.1 Spike,S,477,N,NULL,NULL
JD.1.1 Spike,S,478,K,NULL,NULL
JD.1.1 Spike,S,484,A,NULL,NULL
JD.1.1 Spike,S,486,P,NULL,NULL
JD.1.1 Spike,S,490,S,NULL,NULL
JD.1.1 Spike,S,498,R,NULL,NULL
JD.1.1 Spike,S,501,Y,NULL,NULL
JD.1.1 Spike,S,505,H,NULL,NULL
JD.1.1 Spike,S,614,G,NULL,NULL
JD.1.1 Spike,S,655,Y,NULL,NULL
JD.1.1 Spike,S,679,K,NULL,NULL
JD.1.1 Spike,S,681,H,NULL,NULL
JD.1.1 Spike,S,764,K,NULL,NULL
JD.1.1 Spike,S,796,Y,NULL,NULL
JD.1.1 Spike,S,954,H,NULL,NULL
JD.1.1 Spike,S,969,K,NULL,NULL
JN.1.11.1 Spike,S,19,I,NULL,NULL
JN.1.11.1 Spike,S,21,T,NULL,NULL
JN.1.11.1 Spike,S,24,S,NULL,NULL
JN.1.11.1 Spike,S,25,del,NULL,NULL
JN.1.11.1 Spike,S,26,del,NULL,NULL
JN.1.11.1 Spike,S,27,del,NULL,NULL
JN.1.11.1 Spike,S,50,L,NULL,NULL
JN.1.11.1 Spike,S,69,del,NULL,NULL
JN.1.11.1 Spike,S,70,del,NULL,NULL
JN.1.11.1 Spike,S,127,F,NULL,NULL
JN.1.11.1 Spike,S,142,D,NULL,NULL
JN.1.11.1 Spike,S,144,del,NULL,NULL
JN.1.11.1 Spike,S,157,S,NULL,NULL
JN.1.11.1 Spike,S,158,G,NULL,NULL
JN.1.11.1 Spike,S,211,I,NULL,NULL
JN.1.11.1 Spike,S,212,del,NULL,NULL
JN.1.11.1 Spike,S,213,G,NULL,NULL
JN.1.11.1 Spike,S,216,F,NULL,NULL
JN.1.11.1 Spike,S,245,N,NULL,NULL
JN.1.11.1 Spike,S,264,D,NULL,NULL
JN.1.11.1 Spike,S,332,V,NULL,NULL
JN.1.11.1 Spike,S,339,H,NULL,NULL
JN.1.11.1 Spike,S,356,T,NULL,NULL
JN.1.11.1 Spike,S,371,F,NULL,NULL
JN.1.11.1 Spike,S,373,P,NULL,NULL
JN.1.11.1 Spike,S,375,F,NULL,NULL
JN.1.11.1 Spike,S,376,A,NULL,NULL
JN.1.11.1 Spike,S,403,K,NULL,NULL
JN.1.11.1 Spike,S,405,N,NULL,NULL
JN.1.11.1 Spike,S,408,S,NULL,NULL
JN.1.11.1 Spike,S,417,N,NULL,NULL
JN.1.11.1 Spike,S,440,K,NULL,NULL
JN.1.11.1 Spike,S,445,H,NULL,NULL
JN.1.11.1 Spike,S,446,S,NULL,NULL
JN.1.11.1 Spike,S,450,D,NULL,NULL
JN.1.11.1 Spike,S,452,W,NULL,NULL
JN.1.11.1 Spike,S,455,S,NULL,NULL
JN.1.11.1 Spike,S,456,L,NULL,NULL
JN.1.11.1 Spike,S,460,K,NULL,NULL
JN.1.11.1 Spike,S,477,N,NULL,NULL
JN.1.11.1 Spike,S,478,K,NULL,NULL
JN.1.11.1 Spike,S,481,K,NULL,NULL
JN.1.11.1 Spike,S,483,del,NULL,NULL
JN.1.11.1 Spike,S,484,K,NULL,NULL
JN.1.11.1 Spike,S,486,P,NULL,NULL
JN.1.11.1 Spike,S,498,R,NULL,NULL
JN.1.11.1 Spike,S,501,Y,NULL,NULL
JN.1.11.1 Spike,S,505,H,NULL,NULL
JN.1.11.1 Spike,S,554,K,NULL,NULL
JN.1.11.1 Spike,S,570,V,NULL,NULL
JN.1.11.1 Spike,S,614,G,NULL,NULL
JN.1.11.1 Spike,S,621,S,NULL,NULL
JN.1.11.1 Spike,S,655,Y,NULL,NULL
JN.1.11.1 Spike,S,679,K,NULL,NULL
JN.1.11.1 Spike,S,681,R,NULL,NULL
JN.1.11.1 Spike,S,764,K,NULL,NULL
JN.1.11.1 Spike,S,796,Y,NULL,NULL
JN.1.11.1 Spike,S,939,F,NULL,NULL
JN.1.11.1 Spike,S,954,H,NULL,NULL
JN.1.11.1 Spike,S,969,K,NULL,NULL
JN.1.11.1 Spike,S,1104,L,NULL,NULL
JN.1.11.1 Spike,S,1143,L,NULL,NULL
6 changes: 6 additions & 0 deletions tables/isolates.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1643,6 +1643,7 @@ 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.1.5.1 Spike,Omicron/XBB.1.5.1,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
Expand All @@ -1653,3 +1654,8 @@ XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P+Y453F+N405K,Omicron/XBB.
BA.2.30 Spike,Omicron/BA.2.30,FALSE,NULL,NULL,NULL,TRUE
HV.1 Spike,HV.1,FALSE,NULL,NULL,NULL,TRUE
JN.1 Spike,JN.1,FALSE,NULL,NULL,NULL,TRUE
XBB.2.3 Spike,XBB.2.3,FALSE,NULL,NULL,NULL,TRUE
EU.1.1 Spike,EU.1.1,FALSE,NULL,NULL,NULL,TRUE
HK.3 Spike,HK.3,FALSE,NULL,NULL,NULL,TRUE
JD.1.1 Spike,JD.1.1,FALSE,NULL,NULL,NULL,TRUE
JN.1.11.1 Spike,JN.1.11.1,FALSE,NULL,NULL,NULL,TRUE
43 changes: 34 additions & 9 deletions tables/ref_isolate_pairs/fda24-pair.csv
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,35 @@
ref_name,control_iso_name,iso_name
FDA24,S:614G,B.1.617.2 Spike
FDA24,S:614G,BA.1 Spike
FDA24,S:614G,BA.2 Spike
FDA24,S:614G,BA.4.1 Spike
FDA24,S:614G,XBB.1.16 Spike
FDA24,S:614G,XBB.1.5 Spike
FDA24,S:614G,EG.5.1 Spike
FDA24,S:614G,HV.1 Spike
FDA24,S:614G,JN.1 Spike
FDA24,B.1 Spike,B.1.617.2 Spike
FDA24,B.1 Spike,BA.4.1 Spike
FDA24,B.1 Spike,XBB.1.16 Spike
FDA24,B.1 Spike,XBB.1.5 Spike
FDA24,B.1 Spike,EG.5.1 Spike
FDA24,B.1 Spike,HV.1 Spike
FDA24,B.1 Spike,JN.1 Spike
FDA24,B.1 Spike,B.1.1.7 Spike
FDA24,B.1 Spike,B.1.351 Spike
FDA24,B.1 Spike,P.1 Spike
FDA24,B.1 Spike,B.1.427/9 Spike
FDA24,B.1 Spike,P.2 Spike
FDA24,B.1 Spike,B.1.526/E484K Spike
FDA24,B.1 Spike,B.1.621 Spike
FDA24,B.1 Spike,BA.1 Spike
FDA24,B.1 Spike,BA.2 Spike
FDA24,B.1 Spike,BA.4/5 Spike
FDA24,B.1 Spike,BA.4.6 Spike
FDA24,B.1 Spike,BF.7 Spike
FDA24,B.1 Spike,BQ.1 Spike
FDA24,B.1 Spike,BQ.1.1 Spike
FDA24,B.1 Spike,BA.2.75 Spike
FDA24,B.1 Spike,BN.1 Spike
FDA24,B.1 Spike,XBB Spike
FDA24,B.1 Spike,XBB.1 Spike
FDA24,B.1 Spike,XBB.1.5.10 Spike
FDA24,B.1 Spike,XBB.1.5.1 Spike
FDA24,B.1 Spike,XBB.2.3 Spike
FDA24,B.1 Spike,EU.1.1 Spike
FDA24,B.1 Spike,FL.1.5.1 Spike
FDA24,B.1 Spike,HK.3 Spike
FDA24,B.1 Spike,JD.1.1 Spike
FDA24,B.1 Spike,BA.2.86 Spike
FDA24,B.1 Spike,JN.1.11.1 Spike
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