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Merge pull request #425 from CoVaRR-NET/dev
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Update: 2025-01-24
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@bfjia
bfjia authored Jan 27, 2025
2 parents 05fa451 + deb3c83 commit fa60e5f
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2 changes: 1 addition & 1 deletion DuotangUpdateStatus.json
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{"LastUpdated": "2025-01-17", "LastVirusSeqRelease": "2025-01-16", "LastVirusSeqReleaseID": "4a4f895a-a5f3-4d15-ad1c-173fe12633bb", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1737131619.571149", "Rebuild": "2", "Approved": "False", "LastTreeUpdate": "2025-01-14", "InProgressUpdateDate": "2025-01-17", "FailedCounter": "1", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/423"}
{"LastUpdated": "2025-01-24", "LastVirusSeqRelease": "2025-01-23", "LastVirusSeqReleaseID": "2bf239bc-7ef0-419b-bfd0-5d7bda1b5ea9", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1737738302.111369", "Rebuild": "1", "Approved": "False", "LastTreeUpdate": "2025-01-21", "InProgressUpdateDate": "2025-01-24", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/425"}
14 changes: 7 additions & 7 deletions Tooltip.Rmd
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```{r, echo=FALSE}
tippy::tippy_this(elementId = "XEC", tooltip = "4023 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 = "KP_3_1_1", tooltip = "Ancestor:KP.3.1//10700 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_10_1", tooltip = "Ancestor:MC.10//295 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.10.1, S:A435S, ORF9b:R47H, from sars-cov-2-variants/lineage-proposals#1946")
tippy::tippy_this(elementId = "XEC", tooltip = "4247 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 = "KP_3_1_1", tooltip = "Ancestor:KP.3.1//10300 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_10_1", tooltip = "Ancestor:MC.10//303 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.10.1, S:A435S, ORF9b:R47H, from sars-cov-2-variants/lineage-proposals#1946")
tippy::tippy_this(elementId = "LP_8_1_1", tooltip = "Ancestor:LP.8.1//0 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1, S:K679R, from sars-cov-2-variants/lineage-proposals#2199")
tippy::tippy_this(elementId = "LP_8_1", tooltip = "Ancestor:LP.8//216 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1, S:R190S, from sars-cov-2-variants/lineage-proposals#2199")
tippy::tippy_this(elementId = "KP_1_1", tooltip = "Ancestor:KP.1//13 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_1", tooltip = "Ancestor:KS.1//12 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//254 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//256 samples in last 120 days.//Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1, S:R190S, from sars-cov-2-variants/lineage-proposals#2199")
tippy::tippy_this(elementId = "KP_1_1", tooltip = "Ancestor:KP.1//11 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_1", tooltip = "Ancestor:KS.1//13 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//218 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")
```
147 changes: 82 additions & 65 deletions data_needed/CanPositivityData.csv
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69 changes: 54 additions & 15 deletions downloads/BA.2.tsv
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Expand Up @@ -1932,10 +1932,10 @@
2024-10-14 "JN.1.4" 0 "0%"
2024-10-14 "KP.2.3" 15 "1%"
2024-10-14 "KP.3" 11 "1%"
2024-10-14 "KP.3.1.1" 820 "51%"
2024-10-14 "KP.3.1.1" 820 "50%"
2024-10-14 "LB.1" 3 "0%"
2024-10-14 "MC.1" 183 "11%"
2024-10-14 "other lineages" 591 "36%"
2024-10-14 "other lineages" 592 "36%"
2024-10-21 "BA.2" 0 "0%"
2024-10-21 "BA.2.12.1" 0 "0%"
2024-10-21 "BA.2.3" 0 "0%"
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2024-11-25 "KP.3.1.1" 258 "34%"
2024-11-25 "LB.1" 0 "0%"
2024-11-25 "MC.1" 120 "16%"
2024-11-25 "other lineages" 361 "48%"
2024-11-25 "other lineages" 363 "48%"
2024-12-02 "BA.2" 0 "0%"
2024-12-02 "BA.2.12.1" 0 "0%"
2024-12-02 "BA.2.3" 0 "0%"
Expand All @@ -2022,11 +2022,11 @@
2024-12-02 "JN.1.1" 0 "0%"
2024-12-02 "JN.1.4" 0 "0%"
2024-12-02 "KP.2.3" 3 "0%"
2024-12-02 "KP.3" 8 "1%"
2024-12-02 "KP.3.1.1" 253 "34%"
2024-12-02 "KP.3" 9 "1%"
2024-12-02 "KP.3.1.1" 256 "33%"
2024-12-02 "LB.1" 0 "0%"
2024-12-02 "MC.1" 150 "20%"
2024-12-02 "other lineages" 341 "45%"
2024-12-02 "MC.1" 155 "20%"
2024-12-02 "other lineages" 350 "45%"
2024-12-09 "BA.2" 0 "0%"
2024-12-09 "BA.2.12.1" 0 "0%"
2024-12-09 "BA.2.3" 0 "0%"
Expand All @@ -2035,11 +2035,11 @@
2024-12-09 "JN.1.1" 0 "0%"
2024-12-09 "JN.1.4" 0 "0%"
2024-12-09 "KP.2.3" 0 "0%"
2024-12-09 "KP.3" 5 "1%"
2024-12-09 "KP.3.1.1" 156 "34%"
2024-12-09 "KP.3" 6 "1%"
2024-12-09 "KP.3.1.1" 190 "30%"
2024-12-09 "LB.1" 0 "0%"
2024-12-09 "MC.1" 79 "17%"
2024-12-09 "other lineages" 222 "48%"
2024-12-09 "MC.1" 124 "20%"
2024-12-09 "other lineages" 307 "49%"
2024-12-16 "BA.2" 0 "0%"
2024-12-16 "BA.2.12.1" 0 "0%"
2024-12-16 "BA.2.3" 0 "0%"
Expand All @@ -2048,8 +2048,47 @@
2024-12-16 "JN.1.1" 0 "0%"
2024-12-16 "JN.1.4" 0 "0%"
2024-12-16 "KP.2.3" 0 "0%"
2024-12-16 "KP.3" 0 "0%"
2024-12-16 "KP.3.1.1" 14 "31%"
2024-12-16 "KP.3" 5 "1%"
2024-12-16 "KP.3.1.1" 177 "32%"
2024-12-16 "LB.1" 0 "0%"
2024-12-16 "MC.1" 10 "22%"
2024-12-16 "other lineages" 21 "47%"
2024-12-16 "MC.1" 108 "20%"
2024-12-16 "other lineages" 257 "47%"
2024-12-23 "BA.2" 0 "0%"
2024-12-23 "BA.2.12.1" 0 "0%"
2024-12-23 "BA.2.3" 0 "0%"
2024-12-23 "BA.2.9" 0 "0%"
2024-12-23 "JN.1" 0 "0%"
2024-12-23 "JN.1.1" 0 "0%"
2024-12-23 "JN.1.4" 0 "0%"
2024-12-23 "KP.2.3" 0 "0%"
2024-12-23 "KP.3" 0 "0%"
2024-12-23 "KP.3.1.1" 126 "27%"
2024-12-23 "LB.1" 0 "0%"
2024-12-23 "MC.1" 104 "22%"
2024-12-23 "other lineages" 243 "51%"
2024-12-30 "BA.2" 0 "0%"
2024-12-30 "BA.2.12.1" 0 "0%"
2024-12-30 "BA.2.3" 0 "0%"
2024-12-30 "BA.2.9" 0 "0%"
2024-12-30 "JN.1" 0 "0%"
2024-12-30 "JN.1.1" 0 "0%"
2024-12-30 "JN.1.4" 0 "0%"
2024-12-30 "KP.2.3" 0 "0%"
2024-12-30 "KP.3" 0 "0%"
2024-12-30 "KP.3.1.1" 98 "25%"
2024-12-30 "LB.1" 0 "0%"
2024-12-30 "MC.1" 52 "13%"
2024-12-30 "other lineages" 241 "62%"
2025-01-06 "BA.2" 0 "0%"
2025-01-06 "BA.2.12.1" 0 "0%"
2025-01-06 "BA.2.3" 0 "0%"
2025-01-06 "BA.2.9" 0 "0%"
2025-01-06 "JN.1" 0 "0%"
2025-01-06 "JN.1.1" 0 "0%"
2025-01-06 "JN.1.4" 0 "0%"
2025-01-06 "KP.2.3" 0 "0%"
2025-01-06 "KP.3" 0 "0%"
2025-01-06 "KP.3.1.1" 12 "18%"
2025-01-06 "LB.1" 0 "0%"
2025-01-06 "MC.1" 12 "18%"
2025-01-06 "other lineages" 41 "63%"
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