updates: lit ref & sigs & touch-ups

- Update the reference in README.md to peer-reviewed publication in Nature Microbiology - Signature in sync with what V-pipe is using in production for Wastewater Surveillance in Switzuerland - Commands update in README.md
cbg-ethz · Mar 29, 2023 · 436b520 · 436b520
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diff --git a/README.md b/README.md
@@ -243,9 +243,9 @@ Select a directory containing a collection of virus definitions YAMLs using the
 # fetch the repository of standardised variant definitions
 git clone https://github.com/phe-genomics/variant_definitions.git
 # generate a YAML for omicron subvariant BA.2 using the corresponding standardised variant definitions
-phe2cojac --shortname 'om2' --yaml voc/omicron_ba2_mutations.yaml variant_definitions/variant_yaml/imagines-viewable.yml
+cojac phe2cojac --shortname 'om2' --yaml voc/omicron_ba2_mutations.yaml variant_definitions/variant_yaml/imagines-viewable.yml
 # now have a look at the frequencies of mutations using CoV-Spectrum
-cooc-curate voc/omicron_ba2_mutations.yaml
+cojac cooc-curate voc/omicron_ba2_mutations.yaml
 # adjust the content of the YAML files to your needs
 ```
 
@@ -422,7 +422,7 @@ You can install _cojac_ in its own environment and activate it:
 conda create -n cojac cojac
 conda activate cojac
 # test it
-cojac cooc-mutbamscan --help
+cojac --help
 ```
 
 And to update it to the latest version, run:
@@ -461,7 +461,7 @@ cojac should now be accessible from your PATH
 ```bash
 # activate the environment if not already active:
 conda activate cojac
-cojac cooc-mutbamscan --help
+cojac --help
 ```
 
 ### Remove conda environment
@@ -525,11 +525,11 @@ Long term goal:
 
 If you use this software in your research, please cite:
 
-- Katharina Jahn, David Dreifuss, Ivan Topolsky, Anina Kull, Pravin Ganesanandamoorthy, Xavier Fernandez-Cassi, Carola Bänziger, Elyse Stachler, Lara Fuhrmann, Kim Philipp Jablonski, Chaoran Chen, Catharine Aquino, Tanja Stadler, Christoph Ort, Tamar Kohn, Timothy R. Julian, Niko Beerenwinkel
+- Katharina Jahn, David Dreifuss, Ivan Topolsky, Anina Kull, Pravin Ganesanandamoorthy, Xavier Fernandez-Cassi, Carola Bänziger, Alexander J. Devaux, Elyse Stachler, Lea Caduff, Federica Cariti, Alex Tuñas Corzón, Lara Fuhrmann, Chaoran Chen, Kim Philipp Jablonski, Sarah Nadeau, Mirjam Feldkamp, Christian Beisel, Catharine Aquino, Tanja Stadler, Christoph Ort, Tamar Kohn, Timothy R. Julian & Niko Beerenwinkel
 
-  "*Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples*."
+  "*Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC*."
 
-  medRxiv 2021.01.08.21249379; [doi:10.1101/2021.01.08.21249379](https://doi.org/10.1101/2021.01.08.21249379)
+  Nature Microbiology volume 7, pages 1151–1160 (2022); [doi:10.1038/s41564-022-01185-x](https://doi.org/10.1038/s41564-022-01185-x)
 
 ## Contacts
 

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -60,9 +60,9 @@ def test_workflow():
             "cooc-curate",
             "-a",
             "amplicons.v3.yaml",
-            "voc/omicron_ba2_mutations.yaml",
-            "voc/omicron_ba1_mutations.yaml",
-            "voc/delta_mutations.yaml",
+            "voc/omicron_ba2_mutations_full.yaml",
+            "voc/omicron_ba1_mutations_full.yaml",
+            "voc/delta_mutations_full.yaml",
         ]
     )
     subprocess.check_call(

diff --git a/voc/alpha_mutations.yaml → voc/alpha_mutations_full.yaml b/voc/alpha_mutations.yaml → voc/alpha_mutations_full.yaml
@@ -8,45 +8,44 @@ source:
   - https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563
   - https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201#attachment_4970549
 threshold: 5
+
 mut:
-  # ORF1ab
+  241: 'C>T'
+  913: 'C>T'
+  3037: 'C>T'
   3267: 'C>T' # T1001I
   5388: 'C>A' # A1708D
+  5986: 'C>T'
   6954: 'T>C' # I2230T
-  # S
+  11288: '-----'  # see below:
+  #actually, due to repeated 'T's flanking the region, can be any of these:
+  #11284: '---------' # SGF3675del
+  #11288: '---------' # SGF3675del
+  14408: 'C>T'
+  14676: 'C>T'
+  15279: 'C>T'
+  16176: 'T>C'
+  21765: '------' # T1001I
+  21993: '-'  # see below:
+  #actually, due to repeated 'T's flanking the region, can be any of these:
+  #21991: '---' # 144 -Y
+  #21993: '---' # 144 -Y
   23063: 'A>T' # N501Y !RBD
   23271: 'C>A' # A570D
+  23403: 'A>G'
   23604: 'C>A' # P681H
   23709: 'C>T' # T716I
   24506: 'T>G' # S982A
   24914: 'G>C' # D1118H
-  # ORF8
   27972: 'C>T' # Q27stop
   28048: 'G>T' # R52I
   28111: 'A>G' # Y73C
-  # N
+  28271: '-'
   28280: 'GAT>CTA' # D3L
+  28881: 'GGG>AAC'
   28977: 'C>T' # S235F
-extra:
-  # ORF1ab
-  11288: '---------' # 3675-3677 -SGF
-  913:   'C>T' # syn
-  5986:  'C>T' # syn
-  14676: 'C>T' # syn
-  15279: 'C>T' # syn
-  16176: 'T>C' # syn
-  # S
-  21765: '------' # 69-70 -HV
-  21991: '---' # 144 -Y
-  # M
-  26801: 'T>C' # syn
-
 
-  ## Used by nextclade, but shared with...
-  ## ... 20A / B.1
-  # 8782:  'C'
-  # 14408: 'T'
-  # 23403: 'G'
-  ## ... 20B / B.1.1
-  # 28881: 'A'
-  # 28882: 'A
+#revert:
+  ## used by Nextclade's signatures.
+  #8782:  'C'
+  #26801: 'T>C' # syn
diff --git a/voc/beta_mutations.yaml b/voc/beta_mutations.yaml
diff --git a/voc/beta_mutations_full.yaml b/voc/beta_mutations_full.yaml
@@ -0,0 +1,50 @@
+variant:
+  short: 'be'
+  who: 'beta'
+  pangolin: 'B.1.351'
+  nextstrain: '20H/501Y.V2'
+  voc: 'VOC-202012/02'
+source:
+  - doi:10.1101/2020.12.21.20248640
+  - https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201#attachment_4970549
+threshold: 4
+  # or 5 out of 9 (*)
+mut:
+  174: 'G>T'
+  241: 'C>T'
+  1059: 'C>T' # ORF1ab:T265I
+  3037: 'C>T'
+  5230:  'G>T' # ORF1ab:K1655N (*)
+  10323: 'A>G' # ORF1ab:K3353R
+  11288: '-----'  # see below:
+  #actually, due to repeated 'T's flanking the region, can be any of these:
+  #11284: '---------' # ORF1ab:SGF3675del
+  #11288: '---------' # ORF1ab:SGF3675del
+  14408: 'C>T' # ORF1ab:P4715L
+  21801: 'A>C' # S:D80A (*)
+  22206: 'A>G' # D215G 'not fixed', but determining(*) in source 2
+
+  22287: '---' # see below:
+  #actually, due to repeated 'CTTTAC' motive, can be any of these:
+  #22281: '---------' <- left-most possibility
+  #22283: '---------' <- covspectrum
+  #22286: '---------' <- original pub 'not fixed & un-resolved'
+  #22287: '---------' <- right-most
+  # phegenomics seems wrong due to this causing a mutation 22280: A>C
+  #22280: '---------' <-
+
+  22813: 'G>T' # S:K417N !RBD (*), but source 2 calls it non-determining
+  23012: 'G>A' # S:E484K !RBD
+  23063: 'A>T' # S:N501Y !RBD
+  23403: 'A>G' # S:D614G
+  23664: 'C>T' # S:A701V
+  25563: 'G>T' # ORF3a:Q57H
+  25904: 'C>T' # ORF3a:S171L
+  26456: 'C>T' # E:P71L (*)
+  28253: 'C>T'
+  28887: 'C>T' # N:T205I (*)
+
+#revert:
+  ## Used by nextclade
+  # 8782: 'C'
+
diff --git a/voc/delta_mutations.yaml → voc/delta_mutations_full.yaml b/voc/delta_mutations.yaml → voc/delta_mutations_full.yaml
@@ -9,20 +9,38 @@ source:
 - https://github.com/cov-lineages/pango-designation/issues/49
 threshold: 4
 mut:
-  # S
+  210: 'G>T'
+  241: 'C>T'
+  3037: 'C>T'
+  4181: 'G>T'
+  6402: 'C>T'
+  7124: 'C>T'
+  8986: 'C>T'
+  9053: 'G>T'
+  10029: 'C>T'
+  11201: 'A>G'
+  11332: 'A>G'
+  14408: 'C>T'
+  15451: 'G>A'
+  16466: 'C>T'
+  19220: 'C>T'
   21618: 'C>G' # surface glycoprotein:T19R
+  21987: 'G>A'
+  22029: '------'
   22917: 'T>G' # surface glycoprotein:L452R
   22995: 'C>A' # surface glycoprotein:T478K
+  23403: 'A>G'
   23604: 'C>G' # surface glycoprotein:P681R
   24410: 'G>A' # surface glycoprotein:D950N
-  # ORF3a
   25469: 'C>T' # ORF3a protein:S26L
-  # M
   26767: 'T>C' # membrane glycoprotein:I82T
-  # ORF7a
   27638: 'T>C' # ORF7a protein:V82A
   27752: 'C>T' # ORF7a protein:T120I
-  # N
+  27874: 'C>T'
+  28248: '------'
+  28271: '-'
   28461: 'A>G' # nucleocapsid phosphoprotein:D63G
   28881: 'G>T' # nucleocapsid phosphoprotein:R203M
+  28916: 'G>T'
   29402: 'G>T' # nucleocapsid phosphoprotein:D377Y
+  29742: 'G>T'
diff --git a/voc/gamma_mutations.yaml b/voc/gamma_mutations.yaml
diff --git a/voc/gamma_mutations_full.yaml b/voc/gamma_mutations_full.yaml
@@ -0,0 +1,47 @@
+variant:
+  short: 'ga'
+  who: 'gamma'
+  pangolin: 'P.1'
+  nextstrain: '20J/501Y.V3'
+  voc: 'VOC-202101/02'
+source:
+  - https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
+  - doi:10.1101/2021.02.26.21252554
+  - https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201#attachment_4970549
+threshold: 5
+mut:
+  241: 'C>T'
+  733:  'T>C' # syn
+  2749: 'C>T' # syn
+  3037: 'C>T'
+  3828: 'C>T' # ORF1ab:S1188L
+  5648: 'A>C' # ORF1ab:K1795Q
+  6319: 'A>G'
+  6613: 'A>G'
+  11288: '-----'  # see below:
+  #actually, due to repeated 'T's flanking the region, can be any of these:
+  #11284: '---------' # SGF3675del
+  #11288: '---------' # SGF3675del
+  12778: 'C>T' # syn
+  13860: 'C>T' # syn
+  14408: 'C>T'
+  17259: 'G>T' # ORF1ab:E5665D
+  21614: 'C>T' # S:L18F
+  21621: 'C>A' # S:T20N
+  21638: 'C>T' # S:P26S
+  21974: 'G>T' # S:D138Y
+  22132: 'G>T' # S:R190S
+  22812: 'A>C' # S:K417T !RBD
+  23012: 'G>A' # S:E484K !RBD
+  23063: 'A>T' # S:N501Y !RBD
+  23403: 'A>G'
+  23525: 'C>T' # S:H655Y
+  24642: 'C>T' # S:T1027I
+  25088: 'G>T' # S/1176F
+  26149: 'T>C' # ORF3A/253P
+  28167: 'G>A' # ORF8:E92K
+  28263: '+AACA'
+  28512: 'C>G' # N:P80R
+  28877: 'AG>TC' # N:syn
+  28881: 'GGG>AAC'
+  29834: 'T>A'