Merge pull request #418 from CoVaRR-NET/dev

Update: 2024-12-20

DuotangUpdateStatus.json

@@ -1 +1 @@
-{"LastUpdated": "2024-12-13", "LastVirusSeqRelease": "2024-12-13", "LastVirusSeqReleaseID": "c1f03ce3-37cd-4b17-a203-420eb293350b", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1734104700.428569", "Rebuild": "1", "Approved": "False", "LastTreeUpdate": "2024-12-10", "InProgressUpdateDate": "2024-12-13", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/416"}
+{"LastUpdated": "2024-12-20", "LastVirusSeqRelease": "2024-12-20", "LastVirusSeqReleaseID": "55c2d5e2-e530-489b-9833-7607af3d2683", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1734705917.320679", "Rebuild": "2", "Approved": "False", "LastTreeUpdate": "2024-12-17", "InProgressUpdateDate": "2024-12-20", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/418"}

Tooltip.Rmd

@@ -3,8 +3,11 @@
 
 
 ```{r, echo=FALSE}
-tippy::tippy_this(elementId = "KP_3_1_1", tooltip = "Ancestor:KP.3.1//7008 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1, ORF1a:S4286C, C12616T, S:S31del, Spain, from sars-cov-2-variants/lineage-proposals#1563")
-tippy::tippy_this(elementId = "XEC", tooltip = "1057 samples in last 120 days.//Recombinant lineage of KS.1.1 (JN.1.13.1.1.1) and KP.3.3 (breakpoint 21738-22599), Europe (Germany), from #2717")
-tippy::tippy_this(elementId = "KS_1_1", tooltip = "Ancestor:KS.1//94 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.13.1.1.1, S:T22N, Singapore/Taiwan/Canada, from sars-cov-2-variants/lineage-proposals#1565")
-tippy::tippy_this(elementId = "KP_3_3", tooltip = "Ancestor:KP.3//574 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.3, N:R204P, from sars-cov-2-variants/lineage-proposals#1531")
+tippy::tippy_this(elementId = "XEC", tooltip = "2272 samples in last 120 days.//Recombinant lineage of KS.1.1 (JN.1.13.1.1.1) and KP.3.3 (breakpoint 21738-22599), Europe (Germany), from #2717")
+tippy::tippy_this(elementId = "KS_1_1", tooltip = "Ancestor:KS.1//15 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.13.1.1.1, S:T22N, Singapore/Taiwan/Canada, from sars-cov-2-variants/lineage-proposals#1565")
+tippy::tippy_this(elementId = "KP_3_3", tooltip = "Ancestor:KP.3//442 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.3, N:R204P, from sars-cov-2-variants/lineage-proposals#1531")
+tippy::tippy_this(elementId = "LP_8_1", tooltip = "Ancestor:LP.8//83 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1, S:R190S")
+tippy::tippy_this(elementId = "KP_1_1_3", tooltip = "Ancestor:KP.1.1//241 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1.3, C4999T, many with S:S31del, from sars-cov-2-variants/lineage-proposals#1502")
+tippy::tippy_this(elementId = "KP_3_1_1", tooltip = "Ancestor:KP.3.1//9977 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1, ORF1a:S4286C, C12616T, S:S31del, Spain, from sars-cov-2-variants/lineage-proposals#1563")
+tippy::tippy_this(elementId = "MC_1", tooltip = "Ancestor:KP.3.1.1//1468 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1, S:T572I, from sars-cov-2-variants/lineage-proposals#1638")
 ```

currentsituation.md

@@ -1,12 +1,12 @@
 
 
-<u id='KP_3_1_1'>KP.3.1.1</u> continues to be the most prevalent lineage, with <u id='XEC'>XEC</u> (a recombinant with the KP.3-type spike) becoming more prominent now and still showing the most selective advantage. Any growth though versus <u id='KP_3_1_1'>KP.3.1.1</u> for any variant is still relatively small, verses what has been seen for past notable waves.
-
-
+<u id='XEC'>XEC</u> (a recombinant with the KP.3-type spike) is becoming more prominent now. Any growth to date of all variants is still relatively small, verses what has been seen for past notable waves.
 
 Variants of current interest (due to their current/potential growth advantage, mutations of potential functional significance, or spread in other countries):
 
 * <u id='XEC'>XEC</u> which also has a KP.3-type spike, (recombinant of <u id='KS_1_1'>KS.1.1</u> and <u id='KP_3_3'>KP.3.3</u>) but some changes that appear to confer a slight advantage including immune evasion.
+* <u id='LP_8_1'>LP.8.1</u> (derived from <u id='KP_1_1_3'>KP.1.1.3</u>) - but note it is not showing significant growth in all regions.
+* Additional subvariants of <u id='KP_3_1_1'>KP.3.1.1</u>/<u id='MC_1'>MC.1</u> showing some more recent growth.
 * Plus any highly divergent variants (“saltation” lineages with a sudden increase in number of mutations) and sublineages with additional combinations of mutations identified through mutation scanning (see some references under List of Useful Tools below).
 
 

data_needed/CanPositivityData.csv

@@ -1499,7 +1499,7 @@ Nunavut,62.0,2024,37,2024-09-14,97.0,9.3,1.0
 Canada,1.0,2024,37,2024-09-14,30472.0,18.7,updated
 British Columbia,59.0,2024,38,2024-09-21,3075.0,17.3,updated
 Alberta,48.0,2024,38,2024-09-21,4070.0,12.2,updated
-Saskatchewan,47.0,2024,38,2024-09-21,1404.0,15.7,updated
+Saskatchewan,47.0,2024,38,2024-09-21,1406.0,15.6,updated
 Manitoba,46.0,2024,38,2024-09-21,1105.0,18.0,1.0
 Ontario,35.0,2024,38,2024-09-21,7047.0,18.5,1.0
 Quebec,24.0,2024,38,2024-09-21,11802.0,23.1,updated
@@ -1510,12 +1510,12 @@ Prince Edward Island,11.0,2024,38,2024-09-21,136.0,11.0,1.0
 Yukon,60.0,2024,38,2024-09-21,50.0,12.0,updated
 Northwest Territories,61.0,2024,38,2024-09-21,47.0,12.8,1.0
 Nunavut,62.0,2024,38,2024-09-21,111.0,9.0,1.0
-Canada,1.0,2024,38,2024-09-21,32233.0,18.9,updated
+Canada,1.0,2024,38,2024-09-21,32235.0,18.9,updated
 Alberta,,2024,39,2024-09-28,5249.0,12.0,new
 Alberta,,2024,40,2024-10-05,5212.0,12.2,new
 Alberta,,2024,41,2024-10-12,5535.0,14.7,updated
 Alberta,,2024,42,2024-10-19,5606.0,13.7,updated
-Alberta,,2024,43,2024-10-26,5857.0,12.5,updated
+Alberta,,2024,43,2024-10-26,5854.0,12.5,updated
 Atlantic,,2024,39,2024-09-28,3858.0,16.3,new
 Atlantic,,2024,40,2024-10-05,3825.0,15.2,new
 Atlantic,,2024,41,2024-10-12,3644.0,12.9,new
@@ -1530,7 +1530,7 @@ Canada,,2024,39,2024-09-28,34089.0,17.0,updated
 Canada,,2024,40,2024-10-05,34756.0,16.1,new
 Canada,,2024,41,2024-10-12,34780.0,15.0,updated
 Canada,,2024,42,2024-10-19,34981.0,15.6,updated
-Canada,,2024,43,2024-10-26,35499.0,15.1,updated
+Canada,,2024,43,2024-10-26,35497.0,15.1,updated
 Manitoba,,2024,39,2024-09-28,1327.0,19.5,new
 Manitoba,,2024,40,2024-10-05,1350.0,19.6,new
 Manitoba,,2024,41,2024-10-12,1277.0,16.6,new
@@ -1570,7 +1570,7 @@ Prairies,,2024,39,2024-09-28,7961.0,14.1,updated
 Prairies,,2024,40,2024-10-05,8197.0,14.5,new
 Prairies,,2024,41,2024-10-12,8470.0,16.1,updated
 Prairies,,2024,42,2024-10-19,8498.0,15.0,updated
-Prairies,,2024,43,2024-10-26,9123.0,14.8,updated
+Prairies,,2024,43,2024-10-26,9121.0,14.8,updated
 Prince Edward Island,,2024,39,2024-09-28,161.0,17.4,new
 Prince Edward Island,,2024,40,2024-10-05,196.0,11.2,new
 Prince Edward Island,,2024,41,2024-10-12,172.0,14.0,new
@@ -1585,7 +1585,7 @@ Saskatchewan,,2024,39,2024-09-28,1385.0,17.0,updated
 Saskatchewan,,2024,40,2024-10-05,1635.0,17.6,new
 Saskatchewan,,2024,41,2024-10-12,1658.0,20.6,updated
 Saskatchewan,,2024,42,2024-10-19,1649.0,16.6,updated
-Saskatchewan,,2024,43,2024-10-26,1756.0,18.6,updated
+Saskatchewan,,2024,43,2024-10-26,1757.0,18.6,updated
 Territories,,2024,39,2024-09-28,211.0,7.6,new
 Territories,,2024,40,2024-10-05,145.0,4.8,new
 Territories,,2024,41,2024-10-12,230.0,6.1,new
@@ -1650,51 +1650,68 @@ Yukon,,2024,46,2024-11-16,41.0,0.0,updated
 Alberta,,2024,47,2024-11-23,5930.0,11.5,updated
 Atlantic,,2024,47,2024-11-23,3389.0,6.7,new
 British Columbia,,2024,47,2024-11-23,3428.0,6.0,updated
-Canada,,2024,47,2024-11-23,32615.0,10.2,updated
+Canada,,2024,47,2024-11-23,32618.0,10.2,updated
 Manitoba,,2024,47,2024-11-23,1228.0,13.0,new
 New Brunswick,,2024,47,2024-11-23,1098.0,8.4,new
 Newfoundland and Labrador,,2024,47,2024-11-23,975.0,3.8,new
 Northwest Territories,,2024,47,2024-11-23,38.0,7.9,new
 Nova Scotia,,2024,47,2024-11-23,1209.0,7.6,new
 Nunavut,,2024,47,2024-11-23,122.0,6.6,new
 Ontario,,2024,47,2024-11-23,8053.0,12.4,updated
-Prairies,,2024,47,2024-11-23,8626.0,11.3,updated
+Prairies,,2024,47,2024-11-23,8629.0,11.3,updated
 Prince Edward Island,,2024,47,2024-11-23,107.0,6.5,new
 Quebec,,2024,47,2024-11-23,8916.0,10.3,updated
-Saskatchewan,,2024,47,2024-11-23,1468.0,8.9,updated
+Saskatchewan,,2024,47,2024-11-23,1471.0,9.1,updated
 Territories,,2024,47,2024-11-23,203.0,6.9,new
 Yukon,,2024,47,2024-11-23,43.0,7.0,new
 Alberta,,2024,48,2024-11-30,6049.0,9.8,updated
 Atlantic,,2024,48,2024-11-30,3263.0,6.0,new
 British Columbia,,2024,48,2024-11-30,3413.0,4.7,updated
-Canada,,2024,48,2024-11-30,32166.0,9.7,updated
+Canada,,2024,48,2024-11-30,32173.0,9.7,updated
 Manitoba,,2024,48,2024-11-30,1124.0,10.9,new
 New Brunswick,,2024,48,2024-11-30,1058.0,8.7,new
 Newfoundland and Labrador,,2024,48,2024-11-30,859.0,3.4,new
 Northwest Territories,,2024,48,2024-11-30,25.0,8.0,new
 Nova Scotia,,2024,48,2024-11-30,1200.0,5.7,new
 Nunavut,,2024,48,2024-11-30,83.0,1.2,new
-Ontario,,2024,48,2024-11-30,7962.0,13.5,new
-Prairies,,2024,48,2024-11-30,8614.0,9.5,updated
+Ontario,,2024,48,2024-11-30,7963.0,13.5,updated
+Prairies,,2024,48,2024-11-30,8620.0,9.6,updated
 Prince Edward Island,,2024,48,2024-11-30,146.0,5.5,new
 Quebec,,2024,48,2024-11-30,8781.0,9.8,updated
-Saskatchewan,,2024,48,2024-11-30,1441.0,7.1,updated
+Saskatchewan,,2024,48,2024-11-30,1447.0,7.4,updated
 Territories,,2024,48,2024-11-30,133.0,3.0,updated
 Yukon,,2024,48,2024-11-30,25.0,4.0,updated
-Alberta,,2024,49,2024-12-07,5842.0,9.2,new
-Atlantic,,2024,49,2024-12-07,3033.0,6.6,new
-British Columbia,,2024,49,2024-12-07,3567.0,4.1,new
-Canada,,2024,49,2024-12-07,32114.0,9.2,new
+Alberta,,2024,49,2024-12-07,6240.0,9.2,updated
+Atlantic,,2024,49,2024-12-07,3125.0,6.4,updated
+British Columbia,,2024,49,2024-12-07,3620.0,4.2,updated
+Canada,,2024,49,2024-12-07,32808.0,9.2,updated
 Manitoba,,2024,49,2024-12-07,1132.0,11.5,new
 New Brunswick,,2024,49,2024-12-07,1059.0,6.8,new
 Newfoundland and Labrador,,2024,49,2024-12-07,717.0,2.6,new
 Northwest Territories,,2024,49,2024-12-07,25.0,12.0,new
-Nova Scotia,,2024,49,2024-12-07,1130.0,8.9,new
+Nova Scotia,,2024,49,2024-12-07,1222.0,8.3,updated
 Nunavut,,2024,49,2024-12-07,75.0,8.0,new
-Ontario,,2024,49,2024-12-07,8172.0,13.4,new
-Prairies,,2024,49,2024-12-07,8455.0,9.0,new
+Ontario,,2024,49,2024-12-07,8180.0,13.3,updated
+Prairies,,2024,49,2024-12-07,8927.0,9.2,updated
 Prince Edward Island,,2024,49,2024-12-07,127.0,6.3,new
-Quebec,,2024,49,2024-12-07,8743.0,8.6,new
-Saskatchewan,,2024,49,2024-12-07,1481.0,6.4,new
+Quebec,,2024,49,2024-12-07,8812.0,8.6,updated
+Saskatchewan,,2024,49,2024-12-07,1555.0,7.3,updated
 Territories,,2024,49,2024-12-07,144.0,8.3,new
 Yukon,,2024,49,2024-12-07,44.0,6.8,new
+Alberta,,2024,50,2024-12-14,5990.0,8.7,new
+Atlantic,,2024,50,2024-12-14,3437.0,6.5,new
+British Columbia,,2024,50,2024-12-14,3944.0,5.8,new
+Canada,,2024,50,2024-12-14,34126.0,10.0,new
+Manitoba,,2024,50,2024-12-14,1103.0,8.0,new
+New Brunswick,,2024,50,2024-12-14,1201.0,5.9,new
+Newfoundland and Labrador,,2024,50,2024-12-14,827.0,3.6,new
+Northwest Territories,,2024,50,2024-12-14,34.0,8.8,new
+Nova Scotia,,2024,50,2024-12-14,1273.0,9.3,new
+Nunavut,,2024,50,2024-12-14,128.0,14.1,new
+Ontario,,2024,50,2024-12-14,8936.0,14.8,new
+Prairies,,2024,50,2024-12-14,8509.0,8.0,new
+Prince Edward Island,,2024,50,2024-12-14,136.0,1.5,new
+Quebec,,2024,50,2024-12-14,9106.0,10.3,new
+Saskatchewan,,2024,50,2024-12-14,1416.0,5.1,new
+Territories,,2024,50,2024-12-14,194.0,12.4,new
+Yukon,,2024,50,2024-12-14,32.0,9.4,new