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31
genetics / Re: B.1.1.7 (UK) and B.1.351(SA) and P1(Brazil) and B.1.617(India) and ...
« Last post by gsgs on June 15, 2021, 11:54:17 pm »
weekly promille of B.1.617 in cog-UK-sequences by lab per 2021-06-15
Code: [Select]
oth-,000,003,011,033,046,089,270,432,611,795,837,000
HSLL,000,000,068,232,212,392,470,664,807,893,919,000
RAND,000,032,048,136,228,229,000,160,000,000,000,000
PHEC,000,015,061,083,217,291,380,379,691,795,878,000
MILK,001,004,026,086,160,273,416,602,766,892,899,000
ALDP,000,002,016,049,141,306,507,750,857,929,919,000
CAMC,021,041,081,046,000,000,000,000,000,000,000,000
NORT,000,049,008,020,030,023,089,222,455,650,710,000
LOND,000,000,000,103,117,299,547,672,746,892,895,000
QEUH,000,002,005,009,024,379,706,782,840,906,897,000
CAMB,000,000,041,393,136,331,360,440,968,000,914,000
all-,001,007,022,057,113,227,374,564,752,866,883,000

weekly numbers of all sequences by nation :
all-,2868,8746,7965,7998,7528,7055,7930,9994,13063,19521,4140
SCT,2060,1263,1204,1053,0990,1048,1356,1698,2531,3272,0005
WLS,0364,0351,0262,0205,0190,0162,0181,0175,0139,0272,0212
WLS,0142,0111,0091,0084,0014,0038,0099,0359,0206,0009,0000

weekly promille of B.1.617 by nation :
all,001,007,022,057,113,227,374,564,752,866,883
SCT,000,003,007,027,048,088,313,539,644,755,980
WLS,000,003,004,034,026,111,210,126,503,680,802
WLS,000,000,011,107,142,026,020,053,082,879,000

32
vaccine / effectivity
« Last post by gsgs on June 15, 2021, 01:34:24 am »
Code: [Select]
effectivity in England   1,2 doses

             symp  hosp
BNT-alpha,  47,94  83,95   68,12
AZ--alpha,  49,74  76,86   52,47

BNT-delta,  36,88  94,96   90,66   78
AZ--delta,  30,67  71,92   59,75   65

            40,81  78,92   65,50   71




symp-BNT-alpha,47,94
symp-AZ--alpha,49,74

hosp-BNT-alpha,83,95
hosp-AZ--alpha,76,86

symp-BNT-delta,36,88
symp-AZ--delta,30,67

hosp-BNT-delta,94,96
hosp-AZ--delta,71,92



efficacy

       symp   hosp   death   death|symp

BNT   ,87,95  --,--   
BNT   ,--,90  --,--  --,97   44,--
AZ-   ,--,87         80,--   55,--

BNT>80,       --,93



----------------------------------------------------
PHE-v23.pdf
alpha,symp, 50,88
delta,symp, 33,81

             infe   symp  trans  hosp   death
BNT-alpha,  62,80  62,87  47,--  80,92  77,97
AZ--alpha,  65,--  62,77  42,--  80,--  77,--
----------------------------------------------------
England
BNT-alpha,         47,94         83,95
AZ--alpha,         49,74         76,86

BNT-delta,         36,88         94,96
AZ--delta,         30,67         71,92
----------------------------------------------------
Michigan
10880-0dose,825-1dose,129-2dose

hosp   seve
40,90  -03,16
----------------------------------------------------
Qatar
            infe    seve
BNT-alpha, --,89    --,97
BNT-351  , --,75    --,97
------------------------------------------------






alpha=B.1.1.7  (Kent)
delta=B.1.617.2 (India)
beta?=B.1.351 (South Africa)
gamma?=P.1 (Brazil)
33
nCoV - discussion / Re: Apr07 model UofWA
« Last post by gsgs on June 12, 2021, 10:48:43 pm »
https://www.nature.com/articles/s41467-021-22457-w.pdf

34
actual epidemic charts / Re: UK , London , new variant
« Last post by gsgs on May 29, 2021, 09:28:29 pm »
promille of B.1.617 in sequences at cog-UK by lab and week

Code: [Select]
oth-,000,003,011,035,047,092,282,454,497
HSLL,000,000,068,232,208,392,480,678,000
RAND,000,032,048,136,228,236,000,249,000
PHEC,000,015,061,081,220,291,367,385,713
MILK,001,004,027,085,160,272,420,590,000
ALDP,000,002,016,049,143,307,507,734,000
CAMC,020,041,077,046,000,000,000,000,000
NORT,000,049,008,020,026,028,090,218,476
LOND,000,000,000,103,117,324,579,672,709
QEUH,000,002,005,009,023,376,706,780,000
CAMB,000,000,041,393,136,331,450,440,968
all-,001,007,022,057,115,233,386,560,662



7-day-incidence in UK-regions

Code: [Select]
1927,2747,2831,3015,3210,3425,3846,4340,4298,4514,4524,4493,4340,4038,Bolton
1076,1176,1149,1316,1450,1603,1870,2151,2538,2806,3026,3140,3327,3554,Blackburn with Darwen
0860,1223,1229,1281,1270,1235,1420,1425,1673,1864,1939,2020,2083,1950,Bedford
0586,0900,0946,1006,1050,1099,1123,1226,1268,1335,1373,1401,1442,1459,Glasgow City
0356,0680,0754,0869,0942,1015,1183,1162,1089,1162,1131,1110,1110,1047,East Renfrewshire
0580,0673,0691,0707,0721,0737,0803,0887,0953,0994,1066,1087,1121,1096,Kirklees
0337,0506,0551,0607,0619,0619,0585,0607,0731,0765,0697,0843,0900,0956,Burnley
0357,0454,0530,0552,0573,0562,0508,0595,0757,0692,0811,0811,0822,0909,Midlothian
0879,0992,1064,1038,1077,1011,0939,0879,0859,0780,0806,0747,0714,0694,Derry City and Strabane
0773,1039,1083,1155,1212,1256,1364,1475,1574,1657,1708,1739,1762,1745,top9(0518)
      266,  44,  72,  57,  44, 108, 111,  99,  83,  51,  31,  23, -17,
---------------------------------------------------------------------
0515,0517,0518,0519,0520,0521,0522,0523,0524,0525,0526,0527,0528,0529,

0466,0446,0310,0252,0291,0349,0563,0854,1048,1261,1397,1610,1630,1513,Clackmannanshire
0196,0238,0210,0280,0294,0350,0406,0574,0630,0769,1133,1385,1665,2126,Rossendale
0395,0407,0395,0432,0457,0457,0518,0543,0568,0666,0777,0802,0913,1024,Hyndburn
0179,0201,0223,0262,0268,0279,0341,0402,0514,0570,0648,0776,0821,0972,Renfrewshire
0405,0470,0436,0447,0450,0443,0420,0517,0528,0593,0628,0662,0698,0785,Manchester
0221,0377,0377,0460,0460,0479,0561,0534,0497,0552,0635,0764,0782,0736,East Dunbartonshire
0418,0463,0457,0491,0497,0508,0497,0469,0550,0576,0587,0632,0630,0649,Leicester

0539,0401,0373,0344,0316,0275,0308,0340,0324,0292,0288,0296,0280,0259,Barnsley
0439,0419,0393,0391,0376,0383,0422,0443,0484,0517,0535,0576,0589,0597,Bradford
0194,0283,0293,0319,0382,0435,0461,0555,0571,0613,0644,0654,0660,0723,Bury
0393,0331,0369,0369,0374,0388,0445,0468,0482,0426,0482,0515,0492,0468,Calderdale
0305,0381,0389,0474,0474,0482,0474,0558,0558,0584,0567,0550,0567,0660,Chorley
0181,0154,0154,0154,0134,0141,0147,0161,0188,0254,0315,0429,0522,0623,Dundee City
1803,1135,0685,0555,0485,0407,0373,0364,0338,0295,0286,0251,0208,0208,Erewash
0414,0398,0362,0332,0352,0323,0355,0391,0433,0469,0492,0531,0551,0547,Hillingdon
0490,0567,0578,0593,0563,0512,0508,0475,0501,0516,0508,0538,0545,0527,Hounslow
0208,0237,0231,0287,0327,0304,0315,0366,0417,0423,0383,0394,0462,0513,Kingston upon Thames
0517,0488,0449,0430,0426,0414,0396,0386,0397,0387,0395,0388,0382,0366,Leeds
0314,0314,0296,0324,0361,0422,0418,0498,0512,0498,0479,0451,0422,0441,Luton
0488,0527,0449,0410,0332,0234,0176,0137,0137,0117,0137,0156,0176,0234,Melton
0350,0444,0465,0512,0532,0498,0505,0545,0532,0532,0545,0566,0579,0539,Mid Ulster
0518,0440,0418,0418,0397,0348,0319,0291,0291,0248,0220,0270,0270,0277,Middlesbrough
1002,0689,0584,0595,0480,0407,0365,0344,0240,0209,0146,0146,0177,0136,Moray
0458,0458,0491,0414,0391,0397,0397,0402,0380,0391,0469,0502,0502,0485,Newry Mourne and Down
0252,0267,0252,0282,0267,0304,0304,0349,0482,0438,0438,0468,0490,0557,North Ayrshire
0226,0317,0317,0356,0361,0423,0515,0510,0548,0524,0515,0563,0539,0438,North Tyneside
0358,0413,0445,0391,0402,0380,0423,0445,0521,0499,0478,0489,0554,0695,Pendle
0321,0293,0342,0377,0405,0440,0447,0489,0531,0503,0566,0573,0587,0699,Preston
0101,0081,0067,0081,0087,0074,0087,0101,0141,0188,0255,0303,0437,0558,Reigate and Banstead
0197,0148,0148,0131,0131,0164,0164,0214,0230,0246,0246,0296,0427,0608,Ribble Valley
0477,0432,0423,0427,0396,0396,0436,0436,0472,0459,0472,0522,0558,0625,Rochdale
0321,0255,0251,0247,0259,0255,0247,0274,0340,0325,0340,0406,0440,0556,Salford
0539,0416,0347,0311,0311,0279,0246,0224,0203,0199,0192,0177,0159,0134,Sefton
0695,0530,0497,0563,0475,0508,0475,0430,0441,0419,0364,0386,0298,0265,Selby
0463,0484,0495,0505,0547,0453,0410,0326,0358,0379,0368,0326,0368,0410,South Holland
0265,0387,0462,0471,0484,0459,0424,0434,0440,0468,0477,0462,0499,0555,South Lanarkshire
0312,0295,0303,0345,0371,0358,0417,0493,0560,0569,0543,0535,0552,0527,Trafford
0537,0413,0399,0359,0342,0284,0310,0319,0327,0345,0365,0370,0405,0422,Wakefield
0301,0377,0353,0323,0341,0338,0329,0341,0380,0420,0462,0472,0490,0575,Wigan
0109,0198,0237,0267,0286,0267,0375,0425,0484,0484,0514,0514,0563,0445,Worcester



----,0105,0097,0098,0097,0098,1000,0094,0086,----,0090,0093,0090,0087,Wales
----,0315,0332,0348,0357,0361,0367,0391,0412,----,0438,0450,0467,0492,Scotland
----,0352,0358,0346,0332,0323,0323,0324,0321,----,0332,0334,0323,0309,Northern Ireland
----,0230,0212,0210,0210,0205,0206,0213,0220,----,0231,0236,0241,0248,England
----,0391,0369,0355,0347,0340,0337,0344,0353,----,0368,0375,0376,0373,Yorkshire and the Humber
----,0166,0150,0151,0153,0143,0147,0152,0155,----,0159,0158,0162,0166,West Midlands
----,0116,0097,0094,0092,0086,0085,0082,0085,----,0091,0090,0091,0088,South West
----,0140,0123,0119,0119,0117,0116,0118,0120,----,0122,0125,0133,0144,South East
----,0377,0362,0372,0387,0390,0409,0448,0462,----,0505,0519,0537,0571,North West
----,0219,0203,0200,0195,0186,0197,0197,0199,----,0194,0196,0198,0191,North East
----,0207,0193,0194,0194,0189,0188,0192,0204,----,0215,0220,0227,0231,London
----,0197,0179,0178,0175,0165,0165,0169,0174,----,0179,0186,0190,0186,East of England
----------------------------------------------------------------------
0515,0517,0518,0519,0520,0521,0522,0523,0524,0525,0526,0527,0528,0529


19d,0315,0332,0348,0357,0361,0367,0391,0412,----,0438,0450,0467,0492,Scotland
            17,  16,  09,  04,  06,  24,  21,   ,  26,  12,  17,  25,
27d,0230,0212,0210,0210,0205,0206,0213,0220,----,0231,0236,0241,0248,England
                                01,  07,  07, --,  11,  05,  05,  07,
37d,0166,0150,0151,0153,0143,0147,0152,0155,----,0159,0158,0162,0166,West Midlands
                                04,  05,  03, --,  04,  -1,  04,  04
26d,0140,0123,0119,0119,0117,0116,0118,0120,----,0122,0125,0133,0144,South East
                                     02,  02, --,  02,  03,  08,  11,
17d,0377,0362,0372,0387,0390,0409,0448,0462,----,0505,0519,0537,0571,North West
                 10,  15,  03,  19,  29,  14,  -,  43,  14,  18,  34,
24d,0207,0193,0194,0194,0189,0188,0192,0204,----,0215,0220,0227,0231,London
                                     04,  12,  --,  11,  05,  07,  04




charts : http://magictour.free.fr/bolton.GIF

worldwide : http://magictour.free.fr/e-0528.GIF
increasing since 1-2 weeks in many countries in Asia,South America



35
actual epidemic charts / Re: UK , London , new variant
« Last post by gsgs on May 23, 2021, 01:37:31 am »
promille B.1.617 by lab at cog_uk on 2021-05-22
for weeks 66-73
Code: [Select]
oth-,000,003,010,034,048,080,261,464
HSLL,000,000,068,232,208,392,358,000
RAND,000,032,048,136,228,236,000,000
PHEC,000,015,061,081,233,385,308,304
MILK,001,004,027,085,160,272,420,542
ALDP,000,002,016,049,142,308,469,000
CAMC,020,041,077,046,000,000,000,000
NORT,000,049,008,020,027,029,083,000
LOND,000,000,000,103,117,341,196,000
QEUH,000,002,005,008,023,359,701,000
CAMB,000,000,041,393,142,331,392,000
all-,001,007,022,057,116,238,364,344


7-day-incidence , from 380 UK-regions
Code: [Select]
1927,2747,2831,3015,3210,3425,3846,Bolton
1076,1176,1149,1316,1450,1603,1870,Blackburn with Darwen
0860,1223,1229,1281,1270,1235,1420,Bedford
0586,0900,0946,1006,1050,1099,1123,Glasgow City
0879,0992,1064,1038,1077,1011,0939,Derry City and Strabane
0356,0680,0754,0869,0942,1015,1183,East Renfrewshire
0580,0673,0691,0707,0721,0737,0803,Kirklees
0337,0506,0551,0607,0619,0619,0585,Burnley
0357,0454,0530,0552,0573,0562,0508,Midlothian
0773,1039,1083,1155,1212,1256,1364,top9(0518)
      266,  44,  72,  57,  44, 108
-----------------------------------
0515,0517,0518,0519,0520,0521,0522

0466,0446,0310,0252,0291,0349,0563,Clackmannanshire
0221,0377,0377,0460,0460,0479,0561,East Dunbartonshire
0395,0407,0395,0432,0457,0457,0518,Hyndburn
0226,0317,0317,0356,0361,0423,0515,North Tyneside

0490,0567,0578,0593,0563,0512,0508,Hounslow
0350,0444,0465,0512,0532,0498,0505,Mid Ulster
0517,0488,0449,0430,0426,0414,0396,Leeds
0539,0401,0373,0344,0316,0275,0308,Barnsley
1803,1135,0685,0555,0485,0407,0373,Erewash
0418,0463,0457,0491,0497,0508,0497,Leicester
0488,0527,0449,0410,0332,0234,0176,Melton
0518,0440,0418,0418,0397,0348,0319,Middlesbrough
1002,0689,0584,0595,0480,0407,0365,Moray
0539,0416,0347,0311,0311,0279,0246,Sefton
0695,0530,0497,0563,0475,0508,0475,Selby
0463,0484,0495,0505,0547,0453,0410,South Holland
0537,0413,0399,0359,0342,0284,0310,Wakefield




----,0105,0097,0098,0097,0098,1000,Wales
----,0315,0332,0348,0357,0361,0367,Scotland
----,0352,0358,0346,0332,0323,0323,Northern Ireland
----,0230,0212,0210,0210,0205,0206,England
----,0391,0369,0355,0347,0340,0337,Yorkshire and the Humber
----,0166,0150,0151,0153,0143,0147,West Midlands
----,0116,0097,0094,0092,0086,0085,South West
----,0140,0123,0119,0119,0117,0116,South East
----,0377,0362,0372,0387,0390,0409,North West
----,0219,0203,0200,0195,0186,0197,North East
----,0207,0193,0194,0194,0189,0188,London
----,0197,0179,0178,0175,0165,0165,East of England
-----------------------------------
0515,0517,0518,0519,0520,0521,0522,




5.3% per day , redoubles every 2 weeks currently
in average in the 9 hotspots
36
actual epidemic charts / Re: UK , London , new variant
« Last post by gsgs on May 20, 2021, 12:39:48 pm »
1927,2747,2831,3015,3210,3425,Bolton
1076,1176,1149,1316,1450,1603,Blackburn with Darwen
0860,1223,1229,1281,1270,1235,Bedford
0586,0900,0946,1006,1050,1099,Glasgow City
0879,0992,1064,1038,1077,1011,Derry City and Strabane
0356,0680,0754,0869,0942,1015,East Renfrewshire
0580,0673,0691,0707,0721,0737,Kirklees
0337,0506,0551,0607,0619,0619,Burnley
0357,0454,0530,0552,0573,0562,Midlothian
0773,1039,1083,1155,1212,1256,top9(0518)
-----------------------------------
0515,0517,0518,0519,0520,0521,

0350,0444,0465,0512,0532,0498,Mid Ulster
0418,0463,0457,0491,0497,0508,Leicester

0539,0401,0373,0344,0316,0275,Barnsley
1803,1135,0685,0555,0485,0407,Erewash
0490,0567,0578,0593,0563,0512,Hounslow
0517,0488,0449,0430,0426,0414,Leeds
0488,0527,0449,0410,0332,0234,Melton
0518,0440,0418,0418,0397,0348,Middlesbrough
1002,0689,0584,0595,0480,0407,Moray
0539,0416,0347,0311,0311,0279,Sefton
0695,0530,0497,0563,0475,0508,Selby
0463,0484,0495,0505,0547,0453,South Holland
0537,0413,0399,0359,0342,0284,Wakefield




----,0105,0097,0098,0097,0098,Wales
----,0315,0332,0348,0357,0361,Scotland
----,0352,0358,0346,0332,0323,Northern Ireland
----,0230,0212,0210,0210,0205,England
----,0391,0369,0355,0347,0340,Yorkshire and the Humber
----,0166,0150,0151,0153,0143,West Midlands
----,0116,0097,0094,0092,0086,South West
----,0140,0123,0119,0119,0117,South East
----,0377,0362,0372,0387,0390,North West
----,0219,0203,0200,0195,0186,North East
----,0207,0193,0194,0194,0189,London
----,0197,0179,0178,0175,0165,East of England
-----------------------------------
0515,0517,0518,0519,0520,0521,




5.3% per day , redoubles every 2 weeks currently
in average in the 9 hotspots


37
genetics / Re: table/overview of new variants
« Last post by gsgs on May 16, 2021, 04:09:32 am »
Code: [Select]
HSLL,000,000,068,231,199,406,000
RAND,000,031,047,135,227,240,000
PHEC,000,014,060,081,234,436,052
MILK,000,003,026,082,162,277,000
ALDP,000,002,016,043,142,272,000
CAMC,019,041,077,046,000,000,000
NORT,000,049,007,020,016,022,064
LOND,000,000,000,102,122,341,000
QEUH,000,002,004,008,021,320,000
oth-,000,002,010,038,046,073,155
---------------------------------
week  66, 67, 68, 69, 70, 71, 72


proportion in 0/00 of B.1.617.2 in sequences
at cog-UK in weeks 66-72 by lab (date : 2021-05-15)
(only the 9 labs with the typically most B.1.617)

38
actual epidemic charts / Re: India
« Last post by gsgs on April 25, 2021, 02:07:47 am »
https://whitenewspaper.com/2021/04/24/nearly-60-of-samples-of-indian-variant-from-maha-find-scientists-health-news-et-healthworld/
2021-04-24
both Covaxin and Covishield are able to protect against the strain, reports Sumitra Deb Roy.

all: 15133  (during which time ?)
B.1.1.7 = 1195 (543Punjab, 124Delhi , 29Maha
B.1.617 = 728 (427Maha, 124WB, 75 Delhi , 53Mp)
B.1.351 = 29

----------------------------------------------------------------------------------
Mumbai, peek on 2021-04-04 = 11206 cases
now 5867 cases

---------------------------------------------------------------------

Code: [Select]
Laksha, 7026 ,  0 ,18271 ,  0
Delhi-, 4046 , 17 ,17766 ,160
Goa---, 4434 , 37 , 9560 ,101
Ladakh, 2937 ,  0 , 9554 , 21
Chhatt, 4179 , 32 , 8652 , 96
Mahara,10311 , 47 , 8367 , 58
Chandi, 7914 , 39 , 7579 , 37
Puduch, 3035 , 16 , 7056 , 40
Kerala, 3152 , 17 , 6680 ,  9
DadraN,  817 ,  0 , 4259 ,  3
Karnat, 1611 ,  8 , 4195 , 24
Uttara,  913 ,  5 , 4083 , 34
Haryan, 1587 ,  7 , 4056 , 18
Total#, 1769 ,  9 , 3101 , 19
Himach, 1409 , 15 , 2617 , 29
Gujara, 1132 ,  4 , 2394 , 24
Punjab, 3103 , 57 , 2365 , 34
Madhya,  916 ,  3 , 2182 , 12
Rajast,  501 ,  1 , 2105 ,  9
Andhra,  585 ,  2 , 2064 ,  6
Teleng,  732 ,  3 , 2032 ,  7
TamilN,  980 ,  5 , 2016 ,  8
UttarP,  304 ,  1 , 1938 ,  9
Jharkh,  452 ,  2 , 1853 , 21
JammuK,  837 ,  5 , 1785 ,  8
Sikkim,  321 ,  1 , 1357 ,  1
WestBe,  350 ,  1 , 1332 ,  5
Odisha,  235 ,  0 , 1299 ,  1
Andama,  380 ,  0 , 1190 , 10
Bihar-,  130 ,  0 , 1102 ,  4
Mizora,  149 ,  0 ,  733 ,  1
Meghal,   82 ,  1 ,  532 ,  2
Assam-,   66 ,  0 ,  517 ,  2
Arunac,   28 ,  0 ,  484 ,  0
Manipu,   86 ,  0 ,  313 ,  3
Nagala,   96 ,  0 ,  310 ,  1
Tripur,   75 ,  0 ,  229 ,  0

-------------------------------------

India , COVID 19 by state , per million population
cases- 2021/03/10 - 2021/04/10
deaths 2021/03/10 - 2021/04/10
cases- 2021/04/10 - 2021/04/24
deaths 2021/04/10 - 2021/04/24



https://upload.wikimedia.org/wikipedia/commons/thumb/6/69/India_states_and_union_territories_map.svg/1639px-India_states_and_union_territories_map.svg.png
39
actual epidemic charts / India
« Last post by gsgs on April 17, 2021, 09:58:21 pm »
India updates : https://www.mohfw.gov.in/
Maharashtra dashboard : https://www.covid19maharashtragov.in/mh-covid/dashboard
-----------------------------------------

Maharashtra:3343951 ; 3407245 ; 3458996 ; 3519208 ; 3578160 ; 3639855 ;
3703584,3770707,3839338 , 3898262 , 3960359 , 4094840 , 4228836 , 4343727
4410085,4473394,4539553,4665754

63294,51751,60212,58952,61695,63729,67123,68631
58924(26.6%),62097(23.4%),134481(24.3%),133996(23.8%)
114891(22.4%),66358(23.5%),63329(23.2%),66159(23.0%)
126201(21.8%)
tests,23854185,24075811,24341736,--,24895986,25460008,
25972018,26254737,26527862,26816075,27395288
-----------------------------------------------------


Code: [Select]
daily B.1.617 at cog_uk 0405-0417:
48,--,67,69,69,76,76,
79,79,90,98,140,160,171,
187,---,226,---,---,---,---,
---,441,505,562,---,688,730

Code: [Select]
daily E484Q at cog_UK 0322-0417 :
+50%/w --> more than B.1.1.7 in 15 weeks
064,---,079,086,---,---,---,
088,---,094,098,098,---,106,
109,---,128,130,---,138,138,
142,143,154,163,171,180,184
187,---,203,---,---,---,---,
---,276,298,304,---,322,332

Code: [Select]
daily L452R at cog_UK 0322-0416 :
217,---.263,288,---,---,---,
291,---,340,348,350,---,366,
369,---,452,458,---,487,487,
497,505,536,561,582,607,618
645,---,702,---,---,---,---,
---,981,1052,1115,----,1257,1303

weekly L452R+E484Q : 4,5,14,16,21,34,44,75,51,02
weekly B.1.617 : 4,5,14,18,22,51,99,233,271,13
weekly P.1 : 2,1,3,4,6,10,8,2,11,12,19,14,0
weekly B.1.351 : 08,23,36,59,31,21,29,21,31,38,38,63,90,68,73,61,38,00
weekly B.1.525 : 5,8,15,14,12,16,21,50,55,47,48,26,26,14,21,17,0
weekly B.1.1.318 : 1,4,2,11,6,6,22,14,8,24,14,12,6,10,1
weekly B.1.1.7 : 2407,9870,12943,13300,19156,11687,14101,16452,16136,
14061,16547,16111,17087,12485,8034,7119,4533,114
updated 2021-05-02 , until week 70
-----------------------

B.1.617 / B.1.1.7 : 001,004,012,033,060,114


Code: [Select]
weeks 61,..,69 ; updated on 04-29
B.1.617  ,02,05,14,18,22,51,100,225,125
B.1.351  ,29,38,38,63,90,68,71,56,28
C.36     ,03,15,16,11,09,11,16,24,14
B.1.525  ,43,55,47,48,26,26,14,21,05
P.1      ,04,06,10,08,02,11,12,17,11
B.1.     ,36,39,51,25,27,14,14,18,08
B.1.1.   ,20,25,24,04,12,05,08,08,04
B.1.36.  ,07,04,14,07,02,01,02,07,00
A        ,14,11,08,19,37,14,17,08,03
B.1.1.318,08,24,18,11,28,14,13,06,05
B.1.177  ,167,84,66,30,28,4,11,05,00
B.1.177. ,100,43,25,11,12,4,00,01,00
B.1.36.31,02,08,25,14,05,04,01,00,01
B.1.36   ,06,11,11,07,02,01,00,00,01
B.1.1.7  ,15995,14048,16510,16109,17085,12480,7921,6925,2363

617/117  ,001,004,008,011,013,041,126,325,529, 13.2, 33.1, 82.7, 206.8



{no updates at cog-UK 2021-04-22-2021-04-26}

40
genetics / PRRA
« Last post by gsgs on April 13, 2021, 02:22:47 am »
PRRA [nucleotides CTCCTCGGCGGG or TCCTCGGCGGGC, depending how you align ]
is the amino-acid-furin cleavage site ("FCS") inserted into SARS2 at the S1-S2 border in the spike protein.
It is not seen in the similar bat or pangolin viruses, so ir was speculated that it was
inserted in a lab , as done in similar experiments on IBV=infectious bronchitis virus,
 a coronavirus in birds, for which they are trying to create chicken-vaccines.

there are 2 such FCS in some coronaviruses :

Code: [Select]
CTCCTCGGCGGG = insertion
TCTCCTCGGCGGGCACGT , SARS2  , spike , 2038-2055
  S  P  R  R  A  R
AAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTC , SARS2,spike,2431-2469
  K  P  S  K  R  S  F  I  E  D  L  L  F
AGTCCTAGAAGGCGTTCTTTTATTGAAGACCTTCTATTT , IBV  ,spike,2056-2094,AY761141
  S  P  R  R  R  S  F  I  E  D  L  L  F 

AGTCCTAGAAGGCG
 CTCCTCGGCGGG
 x----x-xx--x


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5413309/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6832359/pdf/viruses-11-00972.pdf


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