Merge pull request #406 from CoVaRR-NET/dev

Update: 2024-11-08
CoVaRR-NET · Nov 12, 2024 · c32f54e · c32f54e
2 parents 730afb8 + bface4c
commit c32f54e
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diff --git a/DuotangUpdateStatus.json b/DuotangUpdateStatus.json
@@ -1 +1 @@
-{"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"}
+{"LastUpdated": "2024-11-08", "LastVirusSeqRelease": "2024-11-08", "LastVirusSeqReleaseID": "07ed7373-0a4e-4681-928f-15b6f0c934cb", "LastViralAIUpdate": "2023-03-15", "LastNotifMessage": "1731078608.019869", "Rebuild": "0", "Approved": "False", "LastTreeUpdate": "2024-11-05", "InProgressUpdateDate": "2024-11-08", "FailedCounter": "0", "PRLink": "https://github.com/CoVaRR-NET/duotang/pull/406"}
diff --git a/data_needed/CanPositivityData.csv b/data_needed/CanPositivityData.csv
diff --git a/data_needed/aligned_allSeqs_sample1.rtt.nwk b/data_needed/aligned_allSeqs_sample1.rtt.nwk
diff --git a/data_needed/aligned_allSeqs_sample1.timetree.nwk b/data_needed/aligned_allSeqs_sample1.timetree.nwk
diff --git a/data_needed/aligned_allSeqs_sample2.rtt.nwk b/data_needed/aligned_allSeqs_sample2.rtt.nwk
diff --git a/data_needed/aligned_allSeqs_sample2.timetree.nwk b/data_needed/aligned_allSeqs_sample2.timetree.nwk
diff --git a/data_needed/aligned_allSeqs_sample3.rtt.nwk b/data_needed/aligned_allSeqs_sample3.rtt.nwk
diff --git a/data_needed/aligned_allSeqs_sample3.timetree.nwk b/data_needed/aligned_allSeqs_sample3.timetree.nwk
diff --git a/data_needed/aligned_nonrecombinant_sample1.rtt.nwk b/data_needed/aligned_nonrecombinant_sample1.rtt.nwk
diff --git a/data_needed/aligned_nonrecombinant_sample1.timetree.nwk b/data_needed/aligned_nonrecombinant_sample1.timetree.nwk
diff --git a/data_needed/aligned_nonrecombinant_sample2.timetree.nwk b/data_needed/aligned_nonrecombinant_sample2.timetree.nwk
diff --git a/data_needed/aligned_nonrecombinant_sample3.timetree.nwk b/data_needed/aligned_nonrecombinant_sample3.timetree.nwk
diff --git a/data_needed/aligned_recombinant_XBBS_sample1.timetree.nwk b/data_needed/aligned_recombinant_XBBS_sample1.timetree.nwk
diff --git a/data_needed/aligned_recombinant_X_sample1.rtt.nwk b/data_needed/aligned_recombinant_X_sample1.rtt.nwk
diff --git a/data_needed/aligned_recombinant_X_sample1.timetree.nwk b/data_needed/aligned_recombinant_X_sample1.timetree.nwk
diff --git a/data_needed/lineageNotes.tsv b/data_needed/lineageNotes.tsv
@@ -1134,6 +1134,12 @@ LB.1.2.3	Alias of B.1.1.529.2.86.1.1.9.2.1.2.3, S:F175L, ORF1a:I1568F, from sars
 LB.1.3	Alias of B.1.1.529.2.86.1.1.9.2.1.3, ORF1b:T1555I
 LB.1.3.1	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1, S:445P, N:T379I, from sars-cov-2-variants/lineage-proposals#1620
 NL.1	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.1, S:R190S, S:C1243F
+NL.2	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.2, ORF1a:T1429I, ORF1a:D1600N, USA
+NL.3	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.3, ORF1a:S2024L, Netherlands, Europe
+NL.4	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.4, ORF1a:H81Y
+NL.5	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.5, ORF1a:M731I, Israel
+NL.6	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.6, S:V1176F, ORF1b:R1687C
+NL.7	Alias of B.1.1.529.2.86.1.1.9.2.1.3.1.7, S:S256L, N:N47Y
 LB.1.3.2	Alias of B.1.1.529.2.86.1.1.9.2.1.3.2, C25413T
 MH.1	Alias of B.1.1.529.2.86.1.1.9.2.1.3.2.1, S:T572I
 LB.1.3.3	Alias of B.1.1.529.2.86.1.1.9.2.1.3.3, S:K182R, from #2723
@@ -1168,6 +1174,8 @@ LP.5	Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.5, S:K478T (rev)
 LP.6	Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.6, S:M153I, C14403T
 LP.7	Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.7, S:R190S
 LP.8	Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8, S:H445R, S:Q493E, S:F186L, ORF3a:P178L, Singapore/Philippines, from #2811
+LP.8.1	Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1, S:R190S
+LP.8.2	Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.2, S:M153I, S:L176F, on ORF1b:P1452L branch
 KP.1.1.4	Alias of B.1.1.529.2.86.1.1.11.1.1.1.4, S:R214H, C11866T, C23929T, from sars-cov-2-variants/lineage-proposals#1593
 KP.1.1.5	Alias of B.1.1.529.2.86.1.1.11.1.1.1.5, S:F59S
 MU.1	Alias of B.1.1.529.2.86.1.1.11.1.1.1.5.1, S:T572I, ORF1a:P4339T, ORF1b:T1902I，from #2676
@@ -1353,6 +1361,7 @@ LF.7	Alias of B.1.1.529.2.86.1.1.16.1.7, S:T22N, S:S31P, S:K182R, S:R190S, S:K44
 LF.7.1	Alias of B.1.1.529.2.86.1.1.16.1.7.1, C6310T
 LF.7.1.1	Alias of B.1.1.529.2.86.1.1.16.1.7.1.1, S:Q677L
 LF.7.1.2	Alias of B.1.1.529.2.86.1.1.16.1.7.1.2, S:A475V, Qatar, #2805
+LF.7.1.3	Alias of B.1.1.529.2.86.1.1.16.1.7.1.3, ORF1a:A1268V, Russia
 LF.7.2	Alias of B.1.1.529.2.86.1.1.16.1.7.2, T20799C
 LF.7.2.1	Alias of B.1.1.529.2.86.1.1.16.1.7.2.1, S:A475V
 LF.7.3	Alias of B.1.1.529.2.86.1.1.16.1.7.3, C17436T
@@ -1366,6 +1375,7 @@ ND.2	Alias of B.1.1.529.2.86.1.1.16.1.8.1.1.2, S:K478E
 ND.3	Alias of B.1.1.529.2.86.1.1.16.1.8.1.1.3, S:K478I, N:S23T, US/NZ
 LF.9	Alias of B.1.1.529.2.86.1.1.16.1.9, S:S60P, from sars-cov-2-variants/lineage-proposals#1718
 LF.9.1	Alias of B.1.1.529.2.86.1.1.16.1.9.1, S:N185D, from sars-cov-2-variants/lineage-proposals#1718
+LF.10	Alias of B.1.1.529.2.86.1.1.16.1.10, S:K182E, C15738T, T29785C, Senegal
 JN.1.16.2	Alias of B.1.1.529.2.86.1.1.16.2, C4777T, from sars-cov-2-variants/lineage-proposals#1253
 LA.1	Alias of B.1.1.529.2.86.1.1.16.2.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1253
 LA.2	Alias of B.1.1.529.2.86.1.1.16.2.2, S:R346I, from sars-cov-2-variants/lineage-proposals#1089
@@ -1426,6 +1436,10 @@ KW.1.2	Alias of B.1.1.529.2.86.1.1.28.1.1.2, S:K529T, Australia
 JN.1.29	Alias of B.1.1.529.2.86.1.1.29, ORF1a:T3224A, after C2644T, Brazil
 JN.1.29.1	Alias of B.1.1.529.2.86.1.1.29.1, S:F456L, from sars-cov-2-variants/lineage-proposals#1253
 MJ.1	Alias of B.1.1.529.2.86.1.1.29.1.1, S:R346T, S:S31P, ORF1a:E2070K
+MJ.1.1	Alias of B.1.1.529.2.86.1.1.29.1.1.1, S:T22N
+MJ.2	Alias of B.1.1.529.2.86.1.1.29.1.2, C8917T, Brazil
+MJ.2.1	Alias of B.1.1.529.2.86.1.1.29.1.2.1, S:R346T, Brazil
+MJ.2.1.1	Alias of B.1.1.529.2.86.1.1.29.1.2.1.1, S:L56V, Brazil
 JN.1.30	Alias of B.1.1.529.2.86.1.1.30, G21255T
 JN.1.30.1	Alias of B.1.1.529.2.86.1.1.30.1, S:R346T, after T7789C, India, from sars-cov-2-variants/lineage-proposals#1089
 KU.1	Alias of B.1.1.529.2.86.1.1.30.1.1, S:K182Q

diff --git a/data_needed/virusseq.metadata.csv.gz b/data_needed/virusseq.metadata.csv.gz