Merge pull request #404 from CoVaRR-NET/dev

Update: 2024-11-01

DuotangUpdateStatus.json

@@ -1 +1 @@
-{"LastUpdated": "2024-10-18", "LastVirusSeqRelease": "2024-10-17", "LastVirusSeqReleaseID": "322f0370-b823-473e-945c-3da7a46a5502", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1729367269.175249", "Rebuild": "0", "Approved": "False", "LastTreeUpdate": "2024-10-18", "InProgressUpdateDate": "2024-10-18", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/400"}
+{"LastUpdated": "2024-11-01", "LastVirusSeqRelease": "2024-10-31", "LastVirusSeqReleaseID": "7049eeb2-391a-43f0-9e51-d6879f8ddc9a", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1730492461.451919", "Rebuild": "1", "Approved": "False", "LastTreeUpdate": "2024-10-29", "InProgressUpdateDate": "2024-11-01", "FailedCounter": "1", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/404"}

Tooltip.Rmd

@@ -3,11 +3,11 @@
 
 
 ```{r, echo=FALSE}
-tippy::tippy_this(elementId = "KP_3_1_1", tooltip = "Ancestor:KP.3.1//3966 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 = "228 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 = "MC_1", tooltip = "Ancestor:KP.3.1.1//209 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")
-tippy::tippy_this(elementId = "KS_1_1", tooltip = "Ancestor:KS.1//118 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//590 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 = "MC_9", tooltip = "Ancestor:KP.3.1.1//159 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.9, ORF3a:K75N, ORF1b:A1219S")
-tippy::tippy_this(elementId = "MC_13", tooltip = "Ancestor:KP.3.1.1//270 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.13, C10681T")
+tippy::tippy_this(elementId = "KP_3_1_1", tooltip = "Ancestor:KP.3.1//5938 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 = "581 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 = "MC_1", tooltip = "Ancestor:KP.3.1.1//411 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")
+tippy::tippy_this(elementId = "MV_1", tooltip = "Ancestor:MB.1.1.1//20 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.49.1.1.1.1.1, S:K478T, India")
+tippy::tippy_this(elementId = "KS_1_1", tooltip = "Ancestor:KS.1//104 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//616 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 = "MC_18", tooltip = "Ancestor:KP.3.1.1//0 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.18, S:N185D, ORF1a:G465S, Spain/Canada")
 ```

currentsituation.md

@@ -1,6 +1,4 @@
-
-
-<u id='KP_3_1_1'>KP.3.1.1</u> is still the most prevalent lineage. Variants growing include <u id='XEC'>XEC</u> (a recombinant with the KP.3-type spike), and subvariants of <u id='KP_3_1_1'>KP.3.1.1</u> (including <u id='MC_1'>MC.1</u> which has S:T572I, and select other MC variants). However data is limited and any growth advantage 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.
+KP.3.1.1 continues to be the most prevalent lineage. <u id='XEC'>XEC</u> (a recombinant with the KP.3-type spike) is showing the most selective advantage / growth now, followed by weaker growth of <u id='MC_1'>MC.1</u> (a <u id='KP_3_1_1'>KP.3.1.1</u> subvariant which has S:T572I). <u id='MV_1'>MV.1</u>, of interest internationally, is showing growth in countries with less <u id='XEC'>XEC</u>, and is not currently showing notable growth in muliple provinces in Canada. Any growth 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.
 
 
 
@@ -9,9 +7,10 @@ Variants of current interest (due to their current/potential growth advantage, m
 
 
 * <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.
-* MC.** variants (<u id='KP_3_1_1'>KP.3.1.1</u> subvariants) including <u id='MC_1'>MC.1</u>, <u id='MC_9'>MC.9</u>, and <u id='MC_13'>MC.13</u>.
+* MC.** variants (<u id='KP_3_1_1'>KP.3.1.1</u> subvariants) including <u id='MC_1'>MC.1</u>, <u id='MC_18'>MC.18</u> (though notable <u id='MC_18'>MC.18</u> growth is not seen in other regions).
+* 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).
+
 
-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).
 
 
 <!-- edited -->