Merge pull request #359 from CoVaRR-NET/dev

Update: 2024-06-10

DuotangUpdateStatus.json

@@ -1 +1 @@
-{"LastUpdated": "2024-05-30", "LastVirusSeqRelease": "2024-05-30", "LastVirusSeqReleaseID": "d141babd-b824-4f8b-a310-717be1f5144f", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1717167408.208269", "Rebuild": "1", "Approved": "False", "LastTreeUpdate": "2024-05-28", "InProgressUpdateDate": "2024-05-30", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/357"}
+{"LastUpdated": "2024-06-10", "LastVirusSeqRelease": "2024-06-06", "LastVirusSeqReleaseID": "3ed3b55a-9096-48bd-95db-aed336055a8a", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1718093188.570089", "Rebuild": "1", "Approved": "False", "LastTreeUpdate": "2024-06-10", "InProgressUpdateDate": "2024-06-10", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/359"}

Tooltip.Rmd

@@ -3,17 +3,18 @@
 
 
 ```{r, echo=FALSE}
-tippy::tippy_this(elementId = "LB_1", tooltip = "Ancestor:LB//44 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.9.2.1, S:F456L (T22928C)")
-tippy::tippy_this(elementId = "KP_3", tooltip = "Ancestor:JN.1.11.1//448 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3, S:Q493E, from sars-cov-2-variants/lineage-proposals#1410")
-tippy::tippy_this(elementId = "JN_1", tooltip = "Ancestor:BA.2.86.1//3919 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1, S:L455S, ORF1a:R3821K, ORF7b:F19L, Europe")
-tippy::tippy_this(elementId = "KP_2", tooltip = "Ancestor:JN.1.11.1//287 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.2, S:R346T on JN.1.11.1 polytomy, from sars-cov-2-variants/lineage-proposals#1089")
-tippy::tippy_this(elementId = "JN_1_11", tooltip = "Ancestor:JN.1//17 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11, S:V1104L, G17334T, India, from #2446")
-tippy::tippy_this(elementId = "JN_1_9", tooltip = "Ancestor:JN.1//113 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.9, S:Q183H, USA/UK/Canada, from #2410")
-tippy::tippy_this(elementId = "KP_2_3", tooltip = "Ancestor:KP.2//24 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.2.3, S:H146Q, ORF3a:K67N, S:31del")
-tippy::tippy_this(elementId = "JN_1_7", tooltip = "Ancestor:JN.1//479 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.7, S:T572I, S:E1150D, USA/France, from sars-cov-2-variants/lineage-proposals#1097")
-tippy::tippy_this(elementId = "KQ_1", tooltip = "Ancestor:JN.1.4.3//8 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.4.3.1, S:R346T, USA from #2487")
-tippy::tippy_this(elementId = "XDK_1", tooltip = "79 samples in last 120 days.//S:R346T, G11596A, from sars-cov-2-variants/lineage-proposals#1407")
-tippy::tippy_this(elementId = "KP_1_1", tooltip = "Ancestor:KP.1//83 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1089")
-tippy::tippy_this(elementId = "KS_1", tooltip = "Ancestor:JN.1.13.1//85 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.13.1.1, S:F456L, from sars-cov-2-variants/lineage-proposals#1253")
+tippy::tippy_this(elementId = "KP_3", tooltip = "Ancestor:JN.1.11.1//581 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3, S:Q493E, from sars-cov-2-variants/lineage-proposals#1410")
+tippy::tippy_this(elementId = "JN_1", tooltip = "Ancestor:BA.2.86.1//3434 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1, S:L455S, ORF1a:R3821K, ORF7b:F19L, Europe")
+tippy::tippy_this(elementId = "JN_1_16_1", tooltip = "Ancestor:JN.1.16//48 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.16.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1089")
+tippy::tippy_this(elementId = "KP_1_1", tooltip = "Ancestor:KP.1//87 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1089")
+tippy::tippy_this(elementId = "KP_2", tooltip = "Ancestor:JN.1.11.1//325 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.2, S:R346T on JN.1.11.1 polytomy, from sars-cov-2-variants/lineage-proposals#1089")
+tippy::tippy_this(elementId = "KS_1", tooltip = "Ancestor:JN.1.13.1//96 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.13.1.1, S:F456L, from sars-cov-2-variants/lineage-proposals#1253")
+tippy::tippy_this(elementId = "LB_1", tooltip = "Ancestor:LB//53 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.9.2.1, S:F456L (T22928C)")
+tippy::tippy_this(elementId = "JN_1_16", tooltip = "Ancestor:JN.1//92 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.16, S:F456L, from sars-cov-2-variants/lineage-proposals#1253")
+tippy::tippy_this(elementId = "JN_1_11", tooltip = "Ancestor:JN.1//16 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11, S:V1104L, G17334T, India, from #2446")
+tippy::tippy_this(elementId = "KP_3_1", tooltip = "Ancestor:KP.3//0 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1, G15372T, A19722G")
+tippy::tippy_this(elementId = "KP_3_2", tooltip = "Ancestor:KP.3//0 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.2, A2611C, C22858T")
+tippy::tippy_this(elementId = "JN_1_13", tooltip = "Ancestor:JN.1//4 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.13, S:A1087S, after C26894T, C25680T, USA, from #2464")
 tippy::tippy_this(elementId = "KZ_1_1_1", tooltip = "Ancestor:KZ.1.1//0 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.1.6.1.1.1, S:T572I from #2548")
+tippy::tippy_this(elementId = "JN_1_9", tooltip = "Ancestor:JN.1//103 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.9, S:Q183H, USA/UK/Canada, from #2410")
 ```

currentsituation.md

@@ -1,24 +1,23 @@
 
 
-Current Situation:
+<u id='KP_3'>KP.3</u> (<u id='JN_1'>JN.1</u> with S:F456L and S:Q493E) is still dominating, however, multiple variants with  S:F456L and S:R346T (aka the “FLiRT” mutations), are still growing as well, in particular <u id='JN_1_16_1'>JN.1.16.1</u>. <u id='KP_1_1'>KP.1.1</u>, <u id='KP_2'>KP.2</u>, <u id='KS_1'>KS.1</u>, and <u id='LB_1'>LB.1</u> and those with the additional S:S31del mutation.
 
-(note a correction in referencing <u id='LB_1'>LB.1</u> plus S:S31del from the last update).
 
 
-
-<u id='KP_3'>KP.3</u> (<u id='JN_1'>JN.1</u> with S:F456L and S:Q493E) is still the most dominant variant in Canada overall. <u id='KP_3'>KP.3</u> has grown most significantly in those regions with less <u id='KP_2'>KP.2</u> (<u id='JN_1_11'>JN.1.11</u> with S:F456L and S:R346T, aka the “FLiRT” mutations), while <u id='KP_2'>KP.2</u> is still quite prevalent in those regions where it appeared first. <u id='LB_1'>LB.1</u> (<u id='JN_1_9'>JN.1.9</u> plus the FLiRT mutations) and <u id='KP_2_3'>KP.2.3</u> (<u id='KP_2'>KP.2</u> plus S:H146Q) - each with S:S31del - are growing significantly in multiple regions globally, and where there wasn’t early introduction and spread of variants like <u id='KP_3'>KP.3</u>.
+Variants of current interest (due to their current/potential growth advantage, mutations of potential functional significance, or spread in other countries):
 
 
 
-Variants of current interest (due to their current/potential growth advantage, mutations of potential functional significance, or spread in other countries):
+(Note re FLiRT variants below how they are described: For example, <u id='JN_1_16_1'>JN.1.16.1</u> is <u id='JN_1_16'>JN.1.16</u> plus S:R346T, but <u id='JN_1_16'>JN.1.16</u> had the other "FLiRT" mutation S:F456L, hence why <u id='JN_1_16_1'>JN.1.16.1</u> is referred to below as <u id='JN_1'>JN.1</u> with the FLiRT mutations, not <u id='JN_1_16'>JN.1.16</u> plus S:R346T.)
 
 
 
-* <u id='JN_1_7'>JN.1.7</u> subvariants and other variants growing that have S:T572I (potentially increases ACE2 binding) with a particular interest with those with also S:R346T like <u id='KQ_1'>KQ.1</u> and <u id='XDK_1'>XDK.1</u> (nicknamed as having “TIRT” mutations).
-* <u id='KP_2'>KP.2</u> (<u id='JN_1_11'>JN.1.11</u> with S:F456L and S:R346T and other variants with these “FLiRT” mutations including also <u id='KP_1_1'>KP.1.1</u> and <u id='KS_1'>KS.1</u>). With a particular interest in those that also have an S:S31del deletion (in particular <u id='KP_2_3'>KP.2.3</u>) or other changes at position 31 in the Spike protein.
-* <u id='KP_3'>KP.3</u> (with S:F456L and S:Q493) which is now the most prevalent variant in Canada overall. Also of particular interest are its subvariants.
+* <u id='JN_1_16_1'>JN.1.16.1</u> (<u id='JN_1'>JN.1</u> with "FLiRT" mutations S:F456L and S:R346T), most notably with the S:S31del deletion.
+* <u id='KP_1_1'>KP.1.1</u> and <u id='KP_2'>KP.2</u> (both <u id='JN_1_11'>JN.1.11</u> with "FLiRT" mutations), most notably with the S:S31del deletion
+* <u id='KP_3'>KP.3</u> (with S:F456L and S:Q493E) which is now the most prevalent variant in Canada overall, plus subvariants <u id='KP_3_1'>KP.3.1</u> and <u id='KP_3_2'>KP.3.2</u>.
+* <u id='KS_1'>KS.1</u> (<u id='JN_1_13'>JN.1.13</u> with FLiRT mutations)
 * <u id='KZ_1_1_1'>KZ.1.1.1</u> (and others with S:F456L, S:R356T and S:T572I - nicknamed a “FLiRTTI” variant.
-* <u id='LB_1'>LB.1</u> (<u id='JN_1_9'>JN.1.9</u> with FLiRT mutations), with S:S31del, and other variants with S:S31del and other mutations at this position 31.
+* <u id='LB_1'>LB.1</u> (<u id='JN_1_9'>JN.1.9</u> with FLiRT mutations), with S:S31del.
 
 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 that are involved in binding or immune evasion. See: