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Variant data reclassification/correction
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@rrohrerdohmh
rrohrerdohmh authored Nov 15, 2024
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51 changes: 51 additions & 0 deletions cases-sequenced.csv
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period_start_date,period_end_date,not_sequenced,sequenced,cases,pct_sequenced,incomplete
01/03/2021,01/30/2021,127534,2565,130099,2,
01/31/2021,02/27/2021,82936,4365,87301,5,
02/28/2021,03/27/2021,76642,5773,82415,7,
03/28/2021,04/24/2021,52850,6788,59638,11,
04/25/2021,05/22/2021,15776,2384,18160,13,
05/23/2021,06/19/2021,4668,674,5342,13,
06/20/2021,07/17/2021,6545,1110,7655,15,
07/18/2021,08/14/2021,28433,5094,33527,15,
08/15/2021,09/11/2021,34426,6049,40475,15,
09/12/2021,10/09/2021,28367,5063,33430,15,
10/10/2021,11/06/2021,17773,3027,20800,15,
11/07/2021,12/04/2021,29626,5215,34841,15,
12/05/2021,01/01/2022,494332,16296,510628,3,
01/02/2022,01/29/2022,424815,19626,444441,4,
01/30/2022,02/26/2022,27788,3193,30981,10,
02/27/2022,03/26/2022,17084,3055,20139,15,
03/27/2022,04/23/2022,40635,7828,48463,16,
04/24/2022,05/21/2022,73592,14578,88170,17,
05/22/2022,06/18/2022,64723,11937,76660,16,
06/19/2022,07/16/2022,76600,13632,90232,15,
07/17/2022,08/13/2022,70737,10455,81192,13,
08/14/2022,09/10/2022,40695,6497,47192,14,
09/11/2022,10/08/2022,38979,5786,44765,13,
10/09/2022,11/05/2022,43904,5389,49293,11,
11/06/2022,12/03/2022,57333,7103,64436,11,
12/04/2022,12/31/2022,70374,6587,76961,9,
01/01/2023,01/28/2023,50763,2619,53382,5,
01/29/2023,02/25/2023,22988,1506,24494,6,
02/26/2023,03/25/2023,10081,1242,11323,11,
03/26/2023,04/22/2023,6261,823,7084,12,
04/23/2023,05/20/2023,4867,715,5582,13,
05/21/2023,06/17/2023,4769,608,5377,11,
06/18/2023,07/15/2023,4657,534,5191,10,
07/16/2023,08/12/2023,10634,1264,11898,11,
08/13/2023,09/09/2023,18708,2689,21397,13,
09/10/2023,10/07/2023,21228,2139,23367,9,
10/08/2023,11/04/2023,10110,1131,11241,10,
11/05/2023,12/02/2023,10546,1162,11708,10,
12/03/2023,12/30/2023,27385,2717,30102,9,
12/31/2023,01/27/2024,31910,2540,34450,7,
01/28/2024,02/24/2024,12849,1440,14289,10,
02/25/2024,03/23/2024,5266,570,5836,10,
03/24/2024,04/20/2024,3307,416,3723,11,
04/21/2024,05/18/2024,3778,476,4254,11,
05/19/2024,06/15/2024,7288,688,7976,9,
06/16/2024,07/13/2024,11712,1479,13191,11,
07/14/2024,08/10/2024,14196,1748,15944,11,
08/11/2024,09/07/2024,9842,1073,10915,10,
09/08/2024,10/05/2024,6566,780,7346,11,
10/06/2024,11/02/2024,2909,292,3201,9,19680
7 changes: 7 additions & 0 deletions now-cases-sequenced.csv
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period_start_date,period_end_date,not_sequenced,sequenced,cases,pct_sequenced,incomplete
05/19/2024,06/15/2024,7288,688,7976,9,
06/16/2024,07/13/2024,11712,1479,13191,11,
07/14/2024,08/10/2024,14196,1748,15944,11,
08/11/2024,09/07/2024,9842,1073,10915,10,
09/08/2024,10/05/2024,6566,780,7346,11,
10/06/2024,11/02/2024,2909,292,3201,9,19680
7 changes: 7 additions & 0 deletions now-variant-epi-data.csv
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"Period start date","Period end date","BA.2 count","BA.2 percent","BA.2.75 count","BA.2.75 percent","JN.1 count","JN.1 percent","JN.1.13.1 count","JN.1.13.1 percent","KP.2 count","KP.2 percent","LB.1 count","LB.1 percent","LB.1.7 count","LB.1.7 percent","KP.3.1.1 count","KP.3.1.1 percent","BQ.1.1 count","BQ.1.1 percent","Omicron other count","Omicron other percent","incomplete"
05/19/2024,06/15/2024,8,1,7,1,223,32,40,6,139,20,83,12,185,27,3,0,0,0,0,0,0
06/16/2024,07/13/2024,5,0,2,0,485,33,44,3,325,22,178,12,341,23,99,7,0,0,0,0,0
07/14/2024,08/10/2024,1,0,5,0,420,24,32,2,474,27,192,11,374,21,250,14,0,0,0,0,0
08/11/2024,09/07/2024,0,0,2,0,230,21,22,2,229,21,134,12,158,15,295,27,1,0,2,0,0
09/08/2024,10/05/2024,0,0,0,0,128,16,40,5,124,16,154,20,57,7,276,35,0,0,1,0,0
10/06/2024,11/02/2024,0,0,0,0,36,12,31,11,25,9,100,34,1,0,99,34,0,0,0,0,19440
13 changes: 13 additions & 0 deletions variant-classification.csv
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variant,name,count,total,percent_in_NYC
B.1.1.529,Omicron,274,274,100
B.1.1.7,Alpha,0,274,0
B.1.351,Beta,0,274,0
B.1.427,Epsilon,0,274,0
B.1.429,Epsilon,0,274,0
B.1.525,Eta,0,274,0
B.1.526,Iota,0,274,0
B.1.617.2,Delta,0,274,0
B.1.621,,0,274,0
P.1,Gamma,0,274,0
P.2,Zeta,0,274,0
Other,,0,274,0
51 changes: 51 additions & 0 deletions variant-epi-data.csv
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"Period start date","Period end date","B.1.526 +E484K count","B.1.526 +E484K percent","B.1.526 no E484K count","B.1.526 no E484K percent","B.1.1.7 count","B.1.1.7 percent","P.1 count","P.1 percent","B.1.427 count","B.1.427 percent","B.1.429 count","B.1.429 percent","B.1.351 count","B.1.351 percent","B.1.617.2 count","B.1.617.2 percent","B.1.621 count","B.1.621 percent","BA.1 count","BA.1 percent","BA.2 count","BA.2 percent","BA.2.12.1 count","BA.2.12.1 percent","BA.2.75 count","BA.2.75 percent","BA.2.86 count","BA.2.86 percent","JN.1 count","JN.1 percent","JN.1.13.1 count","JN.1.13.1 percent","KP.2 count","KP.2 percent","LB.1 count","LB.1 percent","LB.1.7 count","LB.1.7 percent","KP.3.1.1 count","KP.3.1.1 percent","BA.4 count","BA.4 percent","BA.4.6 count","BA.4.6 percent","BA.5 count","BA.5 percent","BF.7 count","BF.7 percent","BQ.1 count","BQ.1 percent","BQ.1.1 count","BQ.1.1 percent","XBB count","XBB percent","XBB.1.5 count","XBB.1.5 percent","XBB.1.9 count","XBB.1.9 percent","EG.5 count","EG.5 percent","HV.1 count","HV.1 percent","FL.1 count","FL.1 percent","XBB.1.16 count","XBB.1.16 percent","Omicron other count","Omicron other percent","Other count","Other percent","incomplete"
01/03/2021,01/30/2021,73,3,225,9,55,2,0,0,22,1,44,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2146,84,
01/31/2021,02/27/2021,439,10,1009,23,410,9,0,0,39,1,76,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2390,55,
02/28/2021,03/27/2021,1164,20,1186,21,1223,21,29,1,28,0,75,1,10,0,4,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2053,36,
03/28/2021,04/24/2021,1559,23,1166,17,2533,37,165,2,34,1,33,0,17,0,7,0,27,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1247,18,
04/25/2021,05/22/2021,341,14,292,12,1034,43,134,6,9,0,5,0,6,0,84,4,49,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,430,18,
05/23/2021,06/19/2021,26,4,26,4,184,27,70,10,0,0,0,0,1,0,132,20,93,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,142,21,
06/20/2021,07/17/2021,3,0,6,1,84,8,49,4,0,0,0,0,1,0,780,70,86,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,101,9,
07/18/2021,08/14/2021,3,0,2,0,23,0,17,0,0,0,0,0,2,0,4949,97,41,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,57,1,
08/15/2021,09/11/2021,0,0,0,0,6,0,8,0,0,0,0,0,0,0,5990,99,25,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20,0,
09/12/2021,10/09/2021,0,0,0,0,0,0,2,0,0,0,0,0,0,0,5039,100,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,
10/10/2021,11/06/2021,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3021,100,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,
11/07/2021,12/04/2021,0,0,0,0,1,0,0,0,0,0,0,0,0,0,5096,98,1,0,86,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,31,1,
12/05/2021,01/01/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3838,24,0,0,12388,76,38,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,32,0,
01/02/2022,01/29/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,132,1,0,0,19392,99,98,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,
01/30/2022,02/26/2022,0,0,0,0,1,0,0,0,0,0,0,0,0,0,8,0,0,0,2834,89,349,11,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,
02/27/2022,03/26/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,874,29,2071,68,101,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,1,0,
03/27/2022,04/23/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,344,4,5537,71,1930,25,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,1,0,
04/24/2022,05/21/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,56,0,5773,40,8472,58,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,115,1,1,0,114,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,41,0,5,0,
05/22/2022,06/18/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,12,0,2041,17,7040,59,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,843,7,101,1,1883,16,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,16,0,0,0,
06/19/2022,07/16/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,394,3,2166,16,2,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1813,13,573,4,8669,64,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10,0,0,0,
07/17/2022,08/13/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,75,1,257,2,15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,800,8,912,9,8355,80,31,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,0,
08/14/2022,09/10/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,14,0,26,0,59,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,212,3,817,13,5236,81,99,2,11,0,1,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,15,0,0,0,
09/11/2022,10/08/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,10,0,12,0,1,0,159,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,73,1,768,13,4015,69,258,4,298,5,166,3,23,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,
10/09/2022,11/05/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,39,1,1,0,293,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,21,0,260,5,1956,36,214,4,1336,25,1035,19,218,4,14,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,
11/06/2022,12/03/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,29,0,0,0,248,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,88,1,900,13,125,2,2307,32,1947,27,852,12,591,8,1,0,0,0,0,0,0,0,0,0,5,0,1,0,
12/04/2022,12/31/2022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,156,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,14,0,291,4,37,1,1049,16,1327,20,752,11,2931,44,11,0,0,0,0,0,0,0,0,0,8,0,0,0,
01/01/2023,01/28/2023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,3,0,0,0,32,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,34,1,2,0,71,3,154,6,103,4,2211,84,1,0,0,0,0,0,0,0,0,0,7,0,0,0,
01/29/2023,02/25/2023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,11,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,12,1,0,0,19,1,26,2,30,2,1395,93,9,1,0,0,0,0,0,0,0,0,1,0,1,0,
02/26/2023,03/25/2023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,13,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,11,1,43,3,30,2,1075,87,53,4,0,0,0,0,1,0,10,1,2,0,0,0,
03/26/2023,04/22/2023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,2,0,0,0,13,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,2,0,7,1,54,7,627,76,75,9,0,0,0,0,0,0,37,4,1,0,0,0,
04/23/2023,05/20/2023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,9,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,49,7,431,60,108,15,4,1,0,0,4,1,107,15,0,0,0,0,
05/21/2023,06/17/2023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,96,16,269,44,72,12,22,4,0,0,5,1,134,22,0,0,0,0,
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