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Embers

Embers: follow emergent SARS-CoV-2 variants over time

Run Geographically Restricted Embers
Last update: Dec 6, 2023

Dates of current data


Delta and Omicron Variants
Global
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Frequencies of Key Pango Lineage Groupings Over Time

Variants and Counts
                                                                                             1111
               1111111111222222222222222222222222223333334444444444444455556666667777788999990112
1122222266777893444455559111111111112444444455555893477770014457788999900471577780016955556882176
8904567979056058234526780122223444452234678901238999613565870627846036815704557911464669049127864
LTTLPPATAHVGTDTDGVYYWEFRRNL---VR---DALALRSYLTPGDWVTGRSSSTDRKNGLSTEFFQGQNYTADHQQNPASTNDNTDQNLSTDVV Counts Percent Lineage
.I..............D..........SGRG.---................D.FPFANSNK._NKA..R.RYH..GY..KH...KY...HK......      0   0.00% Omicron_BA.2+212SGR               
.I.........................---G.---................D.FPFANSNK.RNKAV._.RYH..GY..KH...KY...HK......    479   0.21% Omicron_BA.4andBA.5               
.I..............D..........---G.---................D.FPFANSNK.QNKA..R.RYH..GY..KH.L.KY...HK......      2   0.00% Omicron_BA.2+L452Q+S704L_BA.2.12.1
.I..__..........D..........---G.---................D.FPFANSNK._NKA..R.RYH..GY..KH...KY...HK......      0   0.00% Omicron_BA.2+P25_,P26_            
.I..--..........D..........---G.---................D.FPFANSN..MNKA..R.RYH..GY..KH...KY...HK......      0   0.00% Omicron_BA.2+L452M                
.I..............D..........---G.---................D.FPFANSTK..NKA..R.RYH..GY..KH...KY...HK......      0   0.00% Omicron_BA.2+K417T                
.I..--..........D..........---G.---................D.FPFANSN.._NKA..R.RYH..GY..KH...KY...HK......      7   0.00% Omicron_BA.2                      
........V--...I............---..---................DKLPF.........A..R.RYH..GY..KH...KY...HK......      1   0.00% Omicron_BA.1.1                    
........V--...I............---..---................D_.PF___..._..A..R.RYHK.GY..KH...KYK..HKF.....      0   0.00% Omicron_BA.1                      
........V--...I............---..EPE................D_.PF......_..A..R.RYH..GY..KH...KY...HK......      1   0.00% Omicron_BA.1                      
.R........_..........--G...---..---............._.........._..R.K..........G...*........N........      0   0.00% Delta+FurinRelated                
.R........_..........--G...---..---............._.........._..R.K..........G..*.........N........      0   0.00% Delta+FurinRelated                
.R........_..........--G...---..---............._.........._..R.K..........G.*..........N........      0   0.00% Delta+FurinRelated                
.R........_..........--G...---..---............._.........._..R.K..........G....H.......N........      0   0.00% Delta+FurinRelated                
.R........_..........--G...---..---............._.........._..R.K..........GY...........N........      0   0.00% Delta+FurinRelated                
.R........_..........G--...---..---............._.........._..R.K..........G...*........N........      0   0.00% Delta+FurinRelated                
.R........_..........G--...---..---............._.........._..R.K..........G..*.........N........      0   0.00% Delta+FurinRelated                
.R........_..........G--...---..---............._.........._..R.K..........G.*..........N........      0   0.00% Delta+FurinRelated                
.R........_..........G--...---..---............._.........._..R.K..........G....H.......N........      0   0.00% Delta+FurinRelated                
.R........_..........G--...---..---............._.........._..R.K..........GY...........N........      1   0.00% Delta+FurinRelated                
.R........_...I....H.G--...---..---.V..........._.........._..R.K..........G____R.......N........      0   0.00% Delta+Y145H,A222V                 
.R........_...I....H.--G...---..---.V..........._.........._..R.K..........G____R.......N........      0   0.00% Delta+Y145H,A222V                 
.R........_..._......G--...---..---.V...........__........._..R.K..........G____R.......N......._      1   0.00% Delta+T95_,A222V                  
.R........_..._......--G...---..---.V...........__........._..R.K..........G____R.......N......._      0   0.00% Delta+T95_,A222V                  
.R....._.._..........G--...---..---._.......__.._._........_..R.K_.........G____R.......N......._      2   0.00% Delta                             
.R....._.._..........--G...---..---._.......__.._._........_..R.K_.........G____R.......N......._      0   0.00% Delta                             
........................S..---..---..............................K.....Y...GY...*..............F.      0   0.00% Gamma+FurinRelated                
........................S..---..---..............................K.....Y...GY..*...............F.      0   0.00% Gamma+FurinRelated                
........................S..---..---..............................K.....Y...GY.*................F.      0   0.00% Gamma+FurinRelated                
........................S..---..---..............................K.....Y...GY*.................F.      0   0.00% Gamma+FurinRelated                
........................S..---..---..............................K.....Y...GY____..............F.      0   0.00% Gamma                             
..............I...SN.......---..---.................K............K.....Y...G....H.......N........      0   0.00% Mu                                
...........VI..............---..---......-------..............Q....S.......G...........N.........      0   0.00% Lambda                            
.............A.............---..---G.---...................N.....K.....Y...G.....V...............      1   0.00% Beta                              
.._......--.......-._......---..---....................................Y..DG....H.._........A.H..      0   0.00% Alpha                             
.._......--.......-._......---..---....................................Y..DG....R..I........A.H..      0   0.00% Alpha                             
.._......--......._._......---..---....................................Y..DG....H..I........A.H..      0   0.00% Alpha                             
.._......--.......-._......---..---....................................Y..DG....H..I........A.H..      3   0.00% Alpha                             


The most common sequence patterns that are missed by the varint patterns
Missing: 3747 patterns, for a total of 230162 sequences
                                                                                             1111
               1111111111222222222222222222222222223333334444444444444455556666667777788999990112
1122222266777893444455559111111111112444444455555893477770014457788999900471577780016955556882176
8904567979056058234526780122223444452234678901238999613565870627846036815704557911464669049127864
LTTLPPATAHVGTDTDGVYYWEFRRNL---VR---DALALRSYLTPGDWVTGRSSSTDRKNGLSTEFFQGQNYTADHQQNPASTNDNTDQNLSTDVV Counts Percent NearbyLineage(s)
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______  94082  40.79% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______  38061  16.50% 
_I_---S_________D_-___L____---E_---___________V____HTFPFANSNKSRNKAPS__RYH__GY__KH___KY___HK______  12582   5.45% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KHV__KY___HK______   8950   3.88% 
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______   7840   3.40% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH_L_KY___HK______   7412   3.21% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYHI_GY__KH___KY___HK______   7104   3.08% 
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______   6974   3.02% 
_I_---S_________D_-___L____---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______   3493   1.51% 
_I_---S__--_____D_-___SG_-I---G_---________________H_FPFANSNKSWNKKP___RYH_VGY__KR___KY___HK______   3376   1.46% 
_I_---S_________D___R_L____---G_---________________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______   3080   1.34% 
_I__S___________D_-__G--__S---__---HV_--____________SFPFANSNKSRNKAP___RYH__GY__KH___KY___HK______   1602   0.69% 
_I_---S_________D___R_L____---G_---G_______________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______   1318   0.57% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KHV__KY___HK______   1225   0.53% 
_I_---S_________D_-________---E_---___________V____HTFPFANS_KS_NKAPS__RYH__GY__KH___KY___HK______    980   0.42% 
_I_---S_________D_-________---E_---___________VG___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    909   0.39% 
_I_---S_________D_-________---E_---___________V____HTFPFAN_NKS_NKAPS__RYH__GY__KH___KY___HK______    744   0.32% 
_I__S___________D_-__G--__S---__---HV_--_____________FPFANSNKSMNKAP___RYH__GY__KH___KY___HK______    703   0.30% 
_I_---S_________D__________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    665   0.29% 
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______    511   0.22% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPP__RYH__GY__KRV__KY___HK______    500   0.22% 
_I_---S_________D_-________---E_---___________V____HTFPFANS_KS_NRAPS__RYH__GY__KH___KY___HK______    466   0.20% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NIAPS__RYH__GY__KH___KY___HK______    462   0.20% 
_I_---S_S_______D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KHV__KY___HK______    423   0.18% 
_I_---S_________D_-________---E_---_______H___V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    413   0.18% 
_L_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    395   0.17% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKSQNRAPS__RYH__GY__KH___KY___HK______    321   0.14% 
___---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    315   0.14% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPP__RYH__GY__KH___KY___HK______    303   0.13% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY_HKH___KY___HK______    291   0.13% 
_I_---S_________D__________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______    279   0.12% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______    272   0.12% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKSRNKAPS__RYH__GY__KH___KY___HK______    250   0.11% 
_I_---S_________D_-________---E_---H__________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    250   0.11% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GYK_KH___KY___HK______    242   0.10% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK_____L    241   0.10% 
_I_---S_________D_-________---E_---___________V____HTFPFAN_NKS_NRAPS__RYH__GY__KH___KY___HK______    241   0.10% 
_I_---S_________D_-________---E_---V__________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    235   0.10% 
_I_---S_________D_-________---E_---_V__________G___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    220   0.10% 
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NNAPS__RYH__GY__KH___KY___HK______    209   0.09% 
_I_---S__--_____D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    193   0.08% 
_I_---S_______I_D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    191   0.08% 
_I_---S_________D_-________---E_---H__________V____HTFPFANSNKS_NRAPS__RYH__GY__KH_L_KY___HK______    189   0.08% 
_I_---S_____I___D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    187   0.08% 
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GYH_KH___KY___HK______    183   0.08% 
_I_---S____V____D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    182   0.08% 
FR____________I_D_-_LG--___---G_---____________G___DTFPFANSNKDRNKAP___RYH__GY__KH___KY___HK______    180   0.08% 
_I_---S_________D_-_____S__---E_---____________G___HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______    168   0.07% 
_I_---S_________D_-________---E_---___________V____H_FPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______    168   0.07% 
_I_---S_________D_-________---D_---____________G___HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______    166   0.07% 

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last modified: Wed May 24 14:07 2023



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