diff --git a/defaults/parameters.yaml b/defaults/parameters.yaml index 4a5eae0..e71c40f 100644 --- a/defaults/parameters.yaml +++ b/defaults/parameters.yaml @@ -26,16 +26,6 @@ rule_params: - name: nextclade_recombinants exclude_clades: - "19" # From 2019 - #- "20A" # Non-VoC From 2020 - #- "20B" - #- "20C" - #- "20D" - #- "20E" - #- "20F" - #- "20G" - #- "Alpha" - #- "Beta" - #- "Gamma" # --------------------------------------------------------------------------- # exclude_negatives : true if sequences that are not recombinants (according to Nextclade) should be excluded from sc2rf analysis. @@ -50,32 +40,47 @@ rule_params: exclude_negatives: false max_name_length: 50 clades: + - "20A" # Non-VOC 2020 + - "20B" # Non-VOC 2020 + - "20C" # Non-VOC 2020 + - "20D" # Non-VOC 2020 + - "20E" # Non-VOC 2020 + - "20F" # Non-VOC 2020 + - "20G" # Non-VOC 2020 - "20I" # Alpha - "20H" # Beta - "20J" # Gamma - "21I" # Delta - "21J" # Delta + - "21C" # Episilon + - "21D" # Eta + - "21E" # Theta + - "21B" # Kappa + - "21G" # Lambda + - "21H" # Mu - "21K" # Omicron BA.1 - "21L" # Omicron BA.2 - #- "21B" # Kappa - #- "21C" # Episilon - #- "21D" # Eta - #- "21G" # Lambda - #- "21H" # Mu + - "22A" # Omicron BA.4 + - "22B" # Omicron BA.5 + - "B.1.438.1" # proposed808 mutation_threshold: 0.25 # Note : If you want sc2rf to update its mutation database everytime, add --rebuild-examples to `sc2rf_args`. - sc2rf_args: "--ansi --parents 2-4 --breakpoints 0-10 --unique 1 --max-ambiguous 20 --max-intermission-length 3 --max-intermission-count 3 --ignore-shared" + sc2rf_args: "--ansi --parents 2-100 --breakpoints 0-100 --unique 1 --max-ambiguous 20 --max-intermission-length 3 --max-intermission-count 3 --ignore-shared" debug_args: "--ansi --parents 1-10 --breakpoints 0-100 --unique 1 --max-ambiguous 1000 --max-intermission-length 1 --max-intermission-count 999 --enable-deletions" # --------------------------------------------------------------------------- - # min_len : Ignore recombinants regions shorter than this - # max_parents : Exlude samples with greater than this number of parents - # max_parents : Exlude samples with greater than this number of breakpoints - # motifs : (optional, experimental) Path to a breakpoints motif file + # lapis : If true, query cov-spectrum using LAPIS to identify parental lineages + # : recommended false if number of sequences > 100. + # min_len : (optional) Ignore recombinants regions shorter than this + # max_breakpoints : (optional) Exlude samples with greater than this number of parents + # max_parents : (optional) Exlude samples with greater than this number of breakpoints + # motifs : (optional, experimental) Path to a breakpoints motif file + # lapis - name: sc2rf_recombinants + lapis: true min_len: 1000 max_parents: 2 - max_breakpoints: 2 + max_breakpoints: motifs: # --------------------------------------------------------------------------- diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md index 35c36ab..801811a 100644 --- a/docs/notes/Notes_Development.md +++ b/docs/notes/Notes_Development.md @@ -14,3 +14,11 @@ - Renamed `parents` column to `parents_clade`. - Added `parents_lineage` column. - Restrict `nextclade` output to `fasta,tsv` (alignment and QC table). + +## Params + +- Tested out `--enable-deletions` for `sc2rf` again, caused issues for `XD`, as the first breakpoint no longer contains a breakpoint motif. + +## Data + +- Add proposed771 (BA.5,BA.2) to positive controls. diff --git a/resources/breakpoints.png b/resources/breakpoints.png index 7ae302b..edeb7a9 100644 Binary files a/resources/breakpoints.png and b/resources/breakpoints.png differ diff --git a/resources/breakpoints.svg b/resources/breakpoints.svg index e63edab..722adfa 100644 --- a/resources/breakpoints.svg +++ b/resources/breakpoints.svg @@ -6,7 +6,7 @@ - 2022-07-07T16:50:34.422497 + 2022-07-08T13:50:48.134120 image/svg+xml @@ -39,1289 +39,1289 @@ z - - - + + - - - + + - - - + + - - + - + - + - + - + - + - + @@ -1343,7 +1343,7 @@ L 220.795254 361.335516 L 220.795254 347.069841 L 116.61208 347.069841 z -" clip-path="url(#p1e1f4c3473)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #377eb8"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #377eb8"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #377eb8"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #4daf4a"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #377eb8"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #377eb8"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #4daf4a"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #377eb8"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> +" clip-path="url(#pcea0b1a9b2)" style="fill: #e41a1c"/> - 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+" clip-path="url(#pcea0b1a9b2)" style="fill: #984ea3"/> - +" clip-path="url(#pcea0b1a9b2)" style="fill: #d3d3d3"/> - + @@ -2631,7 +2631,7 @@ z - + @@ -2641,7 +2641,7 @@ z - + @@ -2651,7 +2651,7 @@ z - + @@ -2661,7 +2661,7 @@ z - + @@ -2671,7 +2671,7 @@ z - + @@ -2681,7 +2681,7 @@ z - + @@ -2696,12 +2696,12 @@ z - - + @@ -2711,7 +2711,7 @@ L -3.5 0 - + @@ -2721,7 +2721,7 @@ L -3.5 0 - + @@ -2731,7 +2731,7 @@ L -3.5 0 - + @@ -2741,7 +2741,7 @@ L -3.5 0 - + @@ -2751,7 +2751,7 @@ L -3.5 0 - + @@ -2761,7 +2761,7 @@ L -3.5 0 - + @@ -2771,7 +2771,7 @@ L -3.5 0 - + @@ -2781,7 +2781,7 @@ L -3.5 0 - + @@ -2791,7 +2791,7 @@ L -3.5 0 - + @@ -2801,7 +2801,7 @@ L -3.5 0 - + @@ -2811,7 +2811,7 @@ L -3.5 0 - + @@ -2821,7 +2821,7 @@ L -3.5 0 - + @@ -2831,7 +2831,7 @@ L -3.5 0 - + @@ -2841,37 +2841,37 @@ L -3.5 0 - + - proposed759 + XL - + - XAB + proposed759 - + - XL + XAB - + @@ -2881,7 +2881,7 @@ L -3.5 0 - + @@ -2891,7 +2891,7 @@ L -3.5 0 - + @@ -2901,7 +2901,7 @@ L -3.5 0 - + @@ -2911,7 +2911,7 @@ L -3.5 0 - + @@ -2921,7 +2921,7 @@ L -3.5 0 - + @@ -2931,7 +2931,7 @@ L -3.5 0 - + @@ -2941,7 +2941,7 @@ L -3.5 0 - + @@ -2951,7 +2951,7 @@ L -3.5 0 - + @@ -2961,7 +2961,7 @@ L -3.5 0 - + @@ -2971,7 +2971,7 @@ L -3.5 0 - + @@ -2981,7 +2981,7 @@ L -3.5 0 - + @@ -2991,7 +2991,7 @@ L -3.5 0 - + @@ -3001,7 +3001,7 @@ L -3.5 0 - + @@ -3011,7 +3011,7 @@ L -3.5 0 - + @@ -3021,7 +3021,7 @@ L -3.5 0 - + @@ -3031,7 +3031,7 @@ L -3.5 0 - + @@ -3041,7 +3041,7 @@ L -3.5 0 - + @@ -3051,7 +3051,7 @@ L -3.5 0 - + @@ -3061,7 +3061,7 @@ L -3.5 0 - + @@ -3071,7 +3071,7 @@ L -3.5 0 - + @@ -3081,7 +3081,7 @@ L -3.5 0 - + @@ -3091,7 +3091,7 @@ L -3.5 0 - + @@ -3101,7 +3101,7 @@ L -3.5 0 - + @@ -3111,7 +3111,7 @@ L -3.5 0 - + @@ -3121,7 +3121,7 @@ L -3.5 0 - + @@ -3131,7 +3131,7 @@ L -3.5 0 - + @@ -3141,7 +3141,7 @@ L -3.5 0 - + @@ -3151,7 +3151,7 @@ L -3.5 0 - + @@ -3161,7 +3161,7 @@ L -3.5 0 - + @@ -3171,7 +3171,7 @@ L -3.5 0 - + @@ -3181,7 +3181,7 @@ L -3.5 0 - + @@ -3191,7 +3191,7 @@ L -3.5 0 - + @@ -3201,7 +3201,7 @@ L -3.5 0 - + @@ -3211,7 +3211,7 @@ L -3.5 0 - + @@ -3306,10 +3306,10 @@ L 749.550102 419.293229 - + - + diff --git a/resources/breakpoints.tsv b/resources/breakpoints.tsv index afe9ac4..6153a81 100644 --- a/resources/breakpoints.tsv +++ b/resources/breakpoints.tsv @@ -7,20 +7,20 @@ proposed422 422 NA NA NA proposed437 437 NA NA NA proposed439 439 21988:22577 Delta/21J,Omicron/BA.1/21K NA proposed441 441 21619:21761 Delta/21J,Omicron/BA.1/21K NA -XD 444 21988:22672,25470:25583 Delta/21J,Omicron/BA.1/21K,Delta/21J NA +XD 444 21988:22577,25001:27637 Delta/21J,Omicron/BA.1/21K,Delta/21J NA XF 445 5387:6401 Delta/21J,Omicron/BA.1/21K NA proposed446 446 5585:6511 Delta/21J,Omicron/BA.1/21K NA XG 447 5387:8382 Omicron/BA.1/21K,Omicron/BA.2/21L NA XH 448 10448:11536 Omicron/BA.1/21K,Omicron/BA.2/21L T902C,C904A,G1244A,C22792T,C25624T,C28435T -XJ 449 13196:15239 Omicron/BA.1/21K,Omicron/BA.2/21L NA +XJ 449 13196:15713 Omicron/BA.1/21K,Omicron/BA.2/21L NA XE 454 10448:11536 Omicron/BA.1/21K,Omicron/BA.2/21L C3241T,G5924A,C14599T proposed459 459 NA NA NA XK 460 17411:19954 Omicron/BA.1/21K,Omicron/BA.2/21L NA proposed463 463 13196:15713 Omicron/BA.1/21K,Omicron/BA.2/21L NA -XL 464 6518:8392 Omicron/BA.1/21K,Omicron/BA.2/21L NA +XL 464 5387:8392 Omicron/BA.1/21K,Omicron/BA.2/21L NA proposed467 467 15241:15713 Omicron/BA.1/21K,Omicron/BA.2/21L NA XQ 468 4322:5385 Omicron/BA.1/21K,Omicron/BA.2/21L NA -XR 469 4322:4891 Omicron/BA.1/21K,Omicron/BA.2/21L NA +XR 469 4322:5385 Omicron/BA.1/21K,Omicron/BA.2/21L NA proposed470 470 9209:9343 Omicron/BA.1/21K,Omicron/BA.2/21L NA XS 471 9054:10448 Delta/21J,Omicron/BA.1/21K NA XM 472 17411:19954 Omicron/BA.1/21K,Omicron/BA.2/21L NA @@ -57,7 +57,7 @@ XAG 709 6516:8392 Omicron/BA.2/21L,Omicron/BA.1/21K NA XAH 755 26859:27381 Omicron/BA.2/21L,Omicron/BA.1/21K NA proposed757 757 17413:19953 Omicron/BA.1/21K,Omicron/BA.2/21L NA proposed759 759 5387:8392 Omicron/BA.1/21K,Omicron/BA.2/21L NA -proposed771 771 18163:19862 Omicron/BA.2/21L,Omicron/BA.5/22B NA +proposed771 771 21790:22791 Omicron/BA.2/21L,Omicron/BA.5/22B NA proposed781 781 17411:19954 Omicron/BA.1/21K,Omicron/BA.2/21L NA proposed789 789 26063:26528 Omicron/BA.2/21L,Omicron/BA.1/21K NA proposed798 798 17411:19954 Omicron/BA.1/21K,Omicron/BA.2/21L NA diff --git a/resources/issues.tsv b/resources/issues.tsv index ae728a3..5d0648d 100644 --- a/resources/issues.tsv +++ b/resources/issues.tsv @@ -16,22 +16,22 @@ issue lineage status status_description countries parents_curated breakpoints_cu 478 XT designated South Africa (Gauteng, Limpopo and North-West) Omicron/BA.2/21L,Omicron/BA.1/21K 26062:26528 Likely breakpoint: between 26062 and 26528 (from ORF3a to M protein). South African BA.2/BA.1 Recombinant with S:75V and breakpoint at ORF3a/M Protein (11 Seqs as of 2022-04-10) 2022-03-19T22:27:20Z 2022-04-17T12:12:22Z 2022-04-14T10:19:57Z 472 XM designated Netherlands (NH) Omicron/BA.1/21K,Omicron/BA.2/21L 17411:19954 Likely breakpoint: between 17410 and 19995 (NSP13 or NSP14 or NSP15, ORF1b). Potential BA.1.1/BA.2 Recombinant in the Germany, Netherlands and beyond, with likely breakpoint at NSP13-15 (50 Seqs as of 2022-03-31) 2022-03-16T11:07:00Z 2022-03-31T16:37:53Z 2022-03-31T16:37:39Z 471 XS designated US (CO, ND, DC, OH) Delta/21J,Omicron/BA.1/21K 9054:10448 Likely breakpoint: between 9055 and 10447 (NSP4 or NSP5). Potential Delta/BA.1.1 Recombinant with Likely Breakpoint at NSP4 or NSP5 (37 Seqs in US as of 2022-03-27) 2022-03-12T03:09:20Z 2022-04-01T16:32:20Z 2022-04-01T16:32:08Z -469 XR designated UK (Wales) Omicron/BA.1/21K,Omicron/BA.2/21L 4322:4891 Likely breakpoint: between 4322 and 4891 (NSP3). Potential BA.1.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (43 Seqs in Wales as of 2022-03-11) 2022-03-12T01:50:55Z 2022-04-01T16:31:57Z 2022-04-01T16:31:49Z +469 XR designated UK (Wales) Omicron/BA.1/21K,Omicron/BA.2/21L 4322:5385 Likely breakpoint: between 4322 and 4891 (NSP3). Potential BA.1.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (43 Seqs in Wales as of 2022-03-11) 2022-03-12T01:50:55Z 2022-04-01T16:31:57Z 2022-04-01T16:31:49Z 468 XQ designated UK (England and Wales) Omicron/BA.1/21K,Omicron/BA.2/21L 4322:5385 Likely breakpoint: between 4322 and 5385 (NSP3). Potential BA.1.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (49 Seqs in England and Wales as of 2022-03-27) 2022-03-12T01:21:45Z 2022-04-01T16:31:38Z 2022-04-01T16:31:26Z -464 XL designated UK-England Omicron/BA.1/21K,Omicron/BA.2/21L 6518:8392 Likely breakpoint: between 6518 and 8392 (NSP3). Potential BA.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (38 Seqs in UK as of 2022-03-16) 2022-03-11T17:17:58Z 2022-03-25T16:44:17Z 2022-03-25T16:44:08Z +464 XL designated UK-England Omicron/BA.1/21K,Omicron/BA.2/21L 5387:8392 Likely breakpoint: between 6518 and 8392 (NSP3). Potential BA.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (38 Seqs in UK as of 2022-03-16) 2022-03-11T17:17:58Z 2022-03-25T16:44:17Z 2022-03-25T16:44:08Z 463 XV designated Denmark Omicron/BA.1/21K,Omicron/BA.2/21L 13196:15713 Likely breakpoint: between 13196 and 15713 (NSP10 to NSP12) Potential BA.1/BA.2 Recombinant with Likely Breakpoint at NSP10/NSP12 (28 Sequences in Denmark as of 2022-03-27) 2022-03-11T16:51:36Z 2022-05-11T15:08:41Z 2022-05-11T15:08:17Z 460 XK designated Omicron/BA.1/21K,Omicron/BA.2/21L 17411:19954 Potential recombined BA.2-BA.1.1 lineage in 22 (1.4%) sequences in Roeselare, Belgium characterized by ORF1b:Q866R and ORF1a:R1628C with BA.2 background and ORF1a (2832-10029) and ORF1b (160464-18163) from BA.1.1 (ORF1b:Q866R) 2022-03-10T18:06:31Z 2022-03-25T16:43:43Z 2022-03-25T16:43:23Z 454 XE designated UK (England and Scotland), Ireland Omicron/BA.1/21K,Omicron/BA.2/21L 10448:11536 Likely breakpoint: between 10448 and11287 (NSP5 or NSP6). Potential BA.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP5/NSP6 (267 Sequences in the UK and Ireland) 2022-03-01T02:02:45Z 2022-03-25T22:30:15Z 2022-03-16T17:55:16Z -449 XJ designated Omicron/BA.1/21K,Omicron/BA.2/21L 13196:15239 Eight potential BA.1/BA.2 recombinant sequences with epidemiological linkage were detected in Finland. The recombination breakpoint seems to be downstream from those reported from Denmark (issues #447 and #448 ). Potential BA.1/BA.2 recombinant lineage in Finland [66 seq as of 2022-03-25] 2022-02-21T15:33:27Z 2022-03-25T16:42:59Z 2022-03-25T16:42:48Z +449 XJ designated Omicron/BA.1/21K,Omicron/BA.2/21L 13196:15713 Eight potential BA.1/BA.2 recombinant sequences with epidemiological linkage were detected in Finland. The recombination breakpoint seems to be downstream from those reported from Denmark (issues #447 and #448 ). Potential BA.1/BA.2 recombinant lineage in Finland [66 seq as of 2022-03-25] 2022-02-21T15:33:27Z 2022-03-25T16:42:59Z 2022-03-25T16:42:48Z 448 XH designated Denmark (43 sequences) Omicron/BA.1/21K,Omicron/BA.2/21L 10448:11536 Likely breakpoint: between 10448 and11287 (NSP5 or NSP6). Potential BA.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP5/NSP6 (43 Sequences in Denmark) 2022-02-21T08:51:52Z 2022-03-25T16:41:00Z 2022-03-25T16:40:50Z 447 XG designated Denmark (53 sequences) Omicron/BA.1/21K,Omicron/BA.2/21L 5387:8382 Likely breakpoint: between 5927 and 6511 (NSP3). Potential BA.1/BA.2 Recombinant Lineage with Likely Breakpoint at NSP3 (107 Sequences in Denmark, UK, US and Germany as of 2022/03/02) 2022-02-20T11:58:43Z 2022-03-25T16:40:28Z 2022-03-25T16:39:59Z 445 XF designated UK-England (30 sequences) Delta/21J,Omicron/BA.1/21K 5387:6401 Likely breakpoint: between 5387 and 6511 (NSP3), which is interestingly quite different from other potential Delta/Omicron recombinant lineages. Potential Delta/Omicron Recombinant Lineage with Likely Breakpoint at NSP3 (30 Seqeuences in the UK as of 2022/02/17) 2022-02-19T08:54:51Z 2022-03-16T17:56:16Z 2022-03-16T17:56:05Z -444 XD designated Denmark / France / Netherlands Delta/21J,Omicron/BA.1/21K,Delta/21J 21988:22672,25470:25583 The breakpoint appears to be right before the S gene. Delta (AY.4) and BA.1 recombinant in France/Denmark [~30 seqs, isolated/passaged in Vero] 2022-02-16T19:57:47Z 2022-03-16T17:53:55Z 2022-03-16T17:53:36Z +444 XD designated Denmark / France / Netherlands Delta/21J,Omicron/BA.1/21K,Delta/21J 21988:22577,25001:27637 The breakpoint appears to be right before the S gene. Delta (AY.4) and BA.1 recombinant in France/Denmark [~30 seqs, isolated/passaged in Vero] 2022-02-16T19:57:47Z 2022-03-16T17:53:55Z 2022-03-16T17:53:36Z 263 XC designated Japan Proposal to redesignate None as recombinant lineage X 2021-10-18T05:19:59Z 2021-11-29T17:13:32Z 2021-11-29T17:12:46Z 189 XB designated B.1.627,B.1.628 Proposal to redesignate B.1.631 as recombinant lineage XB 2021-08-16T18:57:43Z 2021-12-16T02:57:45Z 2021-11-22T11:39:05Z 63 XA designated Their parental lineages are B.1.1.7 and B.1.177. The breakpoint location was identified as being between base 21255 and base 21764 in reference coordinates. Proposal to designate a recombinant lineage 2021-04-27T15:53:17Z 2021-05-05T13:43:39Z 2021-05-05T13:42:12Z 608 proposed608 recombinant recombinant proposal Germany (NW, RP, HH), Israel, Norway, UK (England) Omicron/BA.2/21L,Omicron/BA.1/21K 24504:26059 - It has interesting double breakpoints and dual ORF3a substitutions;;Likely breakpoint 1: 24506-26048 (Spike S2/ORF3a);Likely breakpoint 2: 27385-29509 (ORF6/N protein), with S2M deletion. Potential BA.2/BA.1/BA.2 Recombinant with Likely Double Breakpoints (29 Seqs as of 2022-05-06 in Germany, Norway, Israel and UK) 2022-05-07T03:01:50Z 2022-06-16T04:03:31Z NA -514 proposed514 recombinant recombinant proposal Uncertain (travellers arrived in Hong Kong from Germany via the Netherlands) Omicron/BA.1/21K,Omicron/BA.2/21L 20055:21618 Breakpoint: 20055-21618;We detected a recombinant between Omicron subvariants BA.1 and BA.2. It was detected in early Feb from two epidemiologically linked cases. This recombinant has a breakpoint at around the 5' end of spike (20055-21618).;We used Patient 2 sample to clone a RT-PCR product (~2.2k bp) spanning the recombination breakpoint. Both BA.1-specific (19955C/20055A) and BA.2-specific (21618T/21633-21641del) SNPs can be detected in the same plasmid clone, confirming that Patients 1 and 2 were indeed infected by a BA.1/BA.2 recombinant virus. BA.2/BA.1 Recombinant with breakpoint at 20055-21618 detected in travellers arriving in Hong Kong, February 2022 2022-04-02T12:14:42Z 2022-04-09T23:19:13Z NA +514 proposed514 recombinant recombinant proposal Uncertain (travellers arrived in Hong Kong from Germany via the Netherlands) Omicron/BA.1/21K,Omicron/BA.2/21L 20055:21618 Breakpoint: 20055-21618;We detected a recombinant between Omicron subvariants BA.1 and BA.2. It was detected in early Feb from two epidemiologically linked cases. This recombinant has a breakpoint at around the 5' end of spike (20055-21618).;We used Patient 2 sample to clone a RT-PCR product (~2.2k bp) spanning the recombination breakpoint. Both BA.1-specific (19955C/20055A) and BA.2-specific (21618T/21633-21641del) SNPs can be detected in the same plasmid clone, confirming that Patients 1 and 2 were indeed infected by a BA.1/BA.2 recombinant virus. BA.2/BA.1 Recombinant with breakpoint at 20055-21618 detected in travellers arriving in Hong Kong, February 2022 2022-04-02T12:14:42Z 2022-07-08T11:06:05Z NA 484 proposed484 monitor currently too small, watch for future developments Delta/21J,Omicron/BA.2/21L 21619:21761 It looks clean to me, with a single breakpoint at the start of S1. Potential Delta-BA.2 recombinant from Karnataka, India (singlet, 2022-02-11) 2022-03-24T23:20:55Z 2022-05-11T17:08:57Z 2022-05-11T17:08:57Z 701 proposed701 not accepted A proposal for a new lineage has not been accepted Possible recombinant BA.2/A.5 appeared in Asturias. Spain 2022-06-02T17:56:00Z 2022-06-13T11:20:04Z 2022-06-13T11:19:56Z 557 proposed557 not accepted A proposal for a new lineage has not been accepted Canada, Quebec Omicron/BA.1/21K,Omicron/BA.2/21L 11538:12879 Potential BA.1/BA.2 Recombinant with Likely Breakpoint at NSP6-NSP9 (5 Seqs in Canada, Quebec as of 2022-04-13) 2022-04-13T16:52:51Z 2022-06-29T15:42:26Z 2022-04-19T15:28:12Z @@ -49,14 +49,14 @@ issue lineage status status_description countries parents_curated breakpoints_cu 439 proposed439 not accepted A proposal for a new lineage has not been accepted Delta/21J,Omicron/BA.1/21K 21988:22577 Breakpoint: between Spike NTD/RBD nuc 22199-22576 Potential US East Coast BA.1.1/AY.119 recombinant (7 seq) [potentially the one monitored by UKHSA] 2022-02-14T19:09:24Z 2022-05-11T14:33:17Z 2022-05-11T14:33:09Z 422 proposed422 not accepted A proposal for a new lineage has not been accepted Possible English recombinant descended from Omicron and Delta (UKHSA signal under monitoring) 2022-01-31T07:44:42Z 2022-05-11T15:09:41Z 2022-05-11T15:09:34Z 210 proposed210 not accepted A proposal for a new lineage has not been accepted Korea (12 sequences); Korea (9 sequences); Spain (3 sequences), Belgium (1), Germany (1), France (1), Korea ex-UAE (1) 3 small clades with interesting (recombinant-look-alike) mutations 2021-09-06T02:04:47Z 2021-10-12T17:14:00Z 2021-10-12T17:14:00Z -826 proposed826 UK-England (17/19) Likely breakpoint: _to be updated later_ Potential BA.2.12.1 and BA.4.1 recombinant with multiple breakpoints (19 seqs as of 2022-07-07, mainly UK) 2022-07-07T13:28:46Z 2022-07-07T13:40:26Z NA -823 proposed823 Likely breakpoint: between 13195 and 15240 and between 21618 and 21762 German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:S477N, S:H1101Y and 5 other private mutations 2022-07-06T07:10:53Z 2022-07-07T21:11:09Z NA +826 proposed826 UK-England (17/19) Likely breakpoint: _to be updated later_ Potential BA.2.12.1 and BA.4 recombinant with multiple breakpoints (19 seqs as of 2022-07-07, mainly UK) 2022-07-07T13:28:46Z 2022-07-08T17:29:25Z NA +823 proposed823 Likely breakpoint: between 13195 and 15240 and between 21618 and 21762 German BA.2/BA.1/BA.2 recombinant with extra S:K147E, S:R346K, S:H1101Y and 5 other private mutations 2022-07-06T07:10:53Z 2022-07-08T17:00:10Z NA 820 proposed820 Just Denmark for the fast growing main cluster Sublineage/recombinant of a (2nd generation?) BA.5.2.1 with N:P151S and BA.4 or BA.2 in Denmark 2022-07-04T10:50:08Z 2022-07-07T17:44:14Z NA 808 proposed808 2 & 3 - [EPI_ISL_13454711 | EPI_ISL_13454712](https://cov-spectrum.org/explore/Canada/AllSamples/AllTimes/variants?aaMutations=orf1a%3A280v%2Corf1a%3A297v%2Cs%3A373p&) -- Identical genomes, a week apart, from February and March. They are a recombinant between a heavily mutated B.1.438.1 (up to a breakpoint between 18449 and 18877), and BA.1.1.16 for the rest of the genome.;4 - [EPI_ISL_13215742](https://cov-spectrum.org/explore/Canada/AllSamples/AllTimes/variants?aaMutations=orf1a%3A280v%2Cs%3A504s%2Corf1a%3A297v%2Cs%3A494p&) -- Sequence from late April. This one is a more complex recombinant with 5 breakpoints, of the pattern [B.1.438.1 | BA.1.1.16 | B.1.438.1 | BA.1.1.16] | B.1.438.1 | BA.1.1.16].;The 5 breakpoints are [between 10029 and 10449], [15240 and 18163], [23072 and 23525], [between 23854 and 23908], [25551 and 25584]. Chronic B.1.438.1 recombinant with BA.1.1.16 2022-06-28T14:53:45Z 2022-06-28T16:38:02Z NA 798 proposed798 mainly in Canada-BC (67 out of 76), and also found in Hong Kong, India-WB, US-CA, US-WA and Canada-ON. Omicron/BA.1/21K,Omicron/BA.2/21L 17411:19954 Likely breakpoint: between 18166 and 19953 (NSP13/NSP15). It has a similar breakpoint to XM, and thus is clustered next to XM by Usher, however it doesn't have C2470T (which is displayed as a T2470C reversion in Usher tree). Potential BA.1/BA.2 recombinant with likely breakpoint at NSP13/NSP15 (76 Seqs as of 2022-06-25 mainly Canada-BC) 2022-06-26T03:39:27Z 2022-06-26T12:55:25Z NA 789 proposed789 mainly in the US (NV, NC. TX, FL, CA, CO, HI, UT, GA, AK, MI), also found in Mexico, Puerto Rico, Denmark and Japan (1 sequence each) Omicron/BA.2/21L,Omicron/BA.1/21K 26063:26528 Likely breakpoint: between 26063 and 26528 (ORF3a or M protein). Potential BA.2/BA.1 recombinant with likely breakpoint at ORF3a or M (57 Seqs as of 2022-06-23 mainly in the US) 2022-06-24T03:18:39Z 2022-06-24T03:18:39Z NA 781 proposed781 Omicron/BA.1/21K,Omicron/BA.2/21L 17411:19954 Likely breakpoint: between 17410 and 19995 (NSP13 or NSP14 or NSP15, ORF1b).;We noticed the same breakpoint as in XM #757. Potential BA.1/BA.2 Recombinant in Brazil, with a likely breakpoint at NSP13-15 (10 Seqs as of 2022-06-22) 2022-06-22T20:56:10Z 2022-06-22T20:56:10Z NA -771 proposed771 Spain (IB, AS, PV), Denmark and Switzerland Omicron/BA.2/21L,Omicron/BA.5/22B 18163:19862 Likely breakpoint: anywhere downstream of 12160 (or 17822?) and upstream of 21765. Potential BA.2/BA.5.1 recombinant (14 sequences as of 2022-06-27, Spain, Denmark, Canada, Switzerland and the US) 2022-06-18T23:29:21Z 2022-06-28T06:32:27Z NA +771 proposed771 Spain (IB, AS, PV), Denmark and Switzerland Omicron/BA.2/21L,Omicron/BA.5/22B 21790:22791 Likely breakpoint: anywhere downstream of 12160 (or 17822?) and upstream of 21765. Potential BA.2/BA.5.1 recombinant (14 sequences as of 2022-06-27, Spain, Denmark, Canada, Switzerland and the US) 2022-06-18T23:29:21Z 2022-07-08T11:01:44Z NA 759 proposed759 Countries circulating Omicron/BA.1/21K,Omicron/BA.2/21L 5387:8392 New potential recombinant BA.1.1 (lacking G8393A) / BA.2.9 mainly circulanting in Panama identified by the group of Genomic Surveillance of INS-Peru. This potential recombinant presents a breakpoint in the middle of ORF1a. This genomes cannot be assigned by PANGO and are misidentified (unassigned flag) as belong to XQ by NEXTCLADE, however their mutational profile are no compatible with this recombinant lineage. We have recently identified 9 additional genomes from Peru.;sc2rf ouput indicates one breakpoint and identifies BA.1 and BA.2 as parental genomes. New potential recombinant BA.1.1/BA.2.9 mainly circulanting in Panama and other countries (53 genomes) 2022-06-14T20:07:55Z 2022-07-04T17:02:12Z NA 757 proposed757 mainly Germany (51/68 seqs), and also found in Denmark, Slovenia, Netherland, Portugal andSwitzerland. Omicron/BA.1/21K,Omicron/BA.2/21L 17413:19953 "Likely breakpoint: between 17413 and 19953 (NSP13/NSP15);Although, as shown above, this cluster of potential recombinants is assigned as XM by Usher, is also placed perfectly as a sub-branch of XM, and shares identical breakpoint as XM, I however hypothesize that it might be the result of another independent recombination event, considering:;- XM in itself does not have any private mutations to be distinguished from potential similar recombinants, and the breakpoint (between NSP13/NSP15) is a ""hotspot"" according to my personal monitoring of BA.1/BA.2 recombination clusters during recent months;" Potential BA.1/BA.2 recombinant, either XM-like, or potentially a sublineage of XM? (85 sequences as of 2022-06-20 mainly in Germany) 2022-06-14T07:55:39Z 2022-06-20T06:56:42Z NA 646 proposed646 correction Highlight an error in the description or definition India/RJ-SMS-ICMR-INSACOG-TS-11049/2022 has a breakpoint between 12880 and 13195;The six others have their breakpoint between 5386 and 8393 Two differents recombinants lineage for XU in lineages.csv 2022-05-17T07:29:13Z 2022-05-17T18:18:25Z 2022-05-17T18:18:25Z diff --git a/sc2rf b/sc2rf index bc99179..932b590 160000 --- a/sc2rf +++ b/sc2rf @@ -1 +1 @@ -Subproject commit bc99179e828fe7a9a2bdb40ea8fcda9f90ee8a62 +Subproject commit 932b59058e6c57cfd0ad9c526a9d37abb91c58cb diff --git a/workflow/Snakefile b/workflow/Snakefile index ddf8a3b..ee0cabd 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -473,14 +473,32 @@ def _params_sc2rf_recombinants(build): motifs = config["builds"][build]["sc2rf_recombinants"]["motifs"] if motifs: params["motifs"] = "--motifs {}".format(motifs) else: params["motifs"] = "" + + min_len = config["builds"][build]["sc2rf_recombinants"]["min_len"] + if min_len: params["min_len"] = "--min-len {}".format(min_len) + else: params["min_len"] = "" + + max_breakpoints = config["builds"][build]["sc2rf_recombinants"]["max_breakpoints"] + if max_breakpoints: params["max_breakpoints"] = "--max-breakpoints {}".format(max_breakpoints) + else: params["max_breakpoints"] = "" + + max_parents = config["builds"][build]["sc2rf_recombinants"]["max_parents"] + if max_parents: params["max_parents"] = "--max-parents {}".format(max_parents) + else: params["max_parents"] = "" + + lapis = config["builds"][build]["sc2rf_recombinants"]["lapis"] + nextclade_qc = "results/{build}/nextclade_no-recomb/qc.tsv".format(build=build) + if lapis: params["lapis"] = "--nextclade {}".format(nextclade_qc) + else: params["lapis"] = "" + return params # Snakemake rule rule sc2rf_recombinants: - """Post process the sc2rf output to identify recombinants.""" + """Postprocessing the sc2rf output to identify recombinants.""" - message: """Post process the sc2rf output to identify recombinants.\n + message: """Postprocessing the sc2rf output to identify recombinants.\n build: {wildcards.build} log: {log} stats: {output.stats} @@ -502,10 +520,11 @@ rule sc2rf_recombinants: params: outdir = "results/{build}/sc2rf", prefix = "recombinants", - min_len = lambda wildcards: config["builds"][wildcards.build]["sc2rf_recombinants"]["min_len"], - max_parents = lambda wildcards: config["builds"][wildcards.build]["sc2rf_recombinants"]["max_parents"], - max_breakpoints = lambda wildcards: config["builds"][wildcards.build]["sc2rf_recombinants"]["max_breakpoints"], + min_len = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["min_len"], + max_parents = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["max_parents"], + max_breakpoints = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["max_breakpoints"], motifs = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["motifs"], + lapis = lambda wildcards: _params_sc2rf_recombinants(wildcards.build)["lapis"], threads: 1 resources: cpus = 1, @@ -519,15 +538,15 @@ rule sc2rf_recombinants: --csv {input.csv} \ --ansi {input.ansi} \ --prefix {params.prefix} \ - --min-len {params.min_len} \ - --max-parents {params.max_parents} \ - --max-breakpoints {params.max_breakpoints} \ --outdir {params.outdir} \ --aligned {input.alignment} \ --issues {input.issues} \ - --nextclade {input.nextclade} \ --log {log} \ {params.motifs} \ + {params.min_len} \ + {params.max_parents} \ + {params.max_breakpoints} \ + {params.lapis} \ >> {log} 2>&1; # Cleanup