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Merge pull request #66 from cov-lineages/add_xbb
Add xbb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| { | ||
| "label": "XBB-parent1", | ||
| "description": "Majority parent of XBB recombinant lineage", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "mrca_lineage": "", | ||
| "lineage_name": "XBB-parent1", | ||
| "parent_lineage": "BA.2", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "XBB" | ||
| ], | ||
| "note": "Shared mutations with BA.2.75 parent", | ||
| "note": "Likely breakpoint: ~ S:446", | ||
| "sites": [ | ||
| "spike:G339H", | ||
| "spike:G446S", | ||
| "spike:N460K", | ||
| "e:T11A", | ||
| "nuc:C25416T" | ||
| ], | ||
| "rules": { | ||
| "default": { | ||
| "min_alt": 2, | ||
| "max_ref": 2 | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| { | ||
| "label": "XBB-parent2", | ||
| "description": "Minority parent of XBB recombinant lineage", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "mrca_lineage": "", | ||
| "lineage_name": "XBB-parent2", | ||
| "parent_lineage": "XBB-parent1", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "XBB" | ||
| ], | ||
| "note": "Shared mutations with BA.2.10.1 parent", | ||
| "note": "Likely breakpoint: ~ S:446", | ||
| "sites": [ | ||
| "orf1b:S959P" | ||
| ], | ||
| "rules": { | ||
| "default": { | ||
| "min_alt": 0, | ||
| "max_ref": 1 | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| { | ||
| "label": "Omicron (XBB.1.16-like)", | ||
| "description": "XBB.1.16 lineage defining mutations", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "XBB.1.16" | ||
| ], | ||
| "WHO_label": "Omicron", | ||
| "parent_lineage": "XBB.1", | ||
| "mrca_lineage": "XBB.1.16", | ||
| "lineage_name": "XBB.1.16", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "XBB.1.16" | ||
| ], | ||
| "note": "Unique mutations for XBB.1.16 sublineage", | ||
| "sites": [ | ||
| "orf1b:D1746Y", | ||
| "spike:E180V", | ||
| "nuc:T28297C", | ||
| "nuc:A28447G", | ||
| "nuc:C29386T" | ||
| ], | ||
| "rules": { | ||
| "min_alt": 3, | ||
| "max_ref": 1 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| { | ||
| "label": "Omicron (XBB.1.5-like)", | ||
| "description": "XBB.1.5 lineage defining mutations", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "XBB.1.5" | ||
| ], | ||
| "WHO_label": "Omicron", | ||
| "parent_lineage": "XBB.1", | ||
| "mrca_lineage": "XBB.1.5", | ||
| "lineage_name": "XBB.1.5", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "XBB.1.5" | ||
| ], | ||
| "note": "Unique mutations for XBB.1.5 sublineage", | ||
| "sites": [ | ||
| "nuc:T17124C", | ||
| "spike:G252V", | ||
| "spike:F486P" | ||
| ], | ||
| "rules": { | ||
| "min_alt": 2, | ||
| "max_ref": 0, | ||
| "spike:F486":"alt" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| { | ||
| "label": "Omicron (XBB.1-like)", | ||
| "description": "XBB.1 lineage defining mutations", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "XBB.1" | ||
| ], | ||
| "WHO_label": "Omicron", | ||
| "parent_lineage": "XBB", | ||
| "mrca_lineage": "XBB.1", | ||
| "lineage_name": "XBB.1", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "XBB.1" | ||
| ], | ||
| "note": "Unique mutations for XBB.1 sublineage", | ||
| "sites": [ | ||
| "spike:R408S", | ||
| "spike:K417N", | ||
| "orf8:G8*" | ||
| ], | ||
| "rules": { | ||
| "min_alt": 2, | ||
| "max_ref": 0 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| { | ||
| "label": "Omicron (XBB-like)", | ||
| "description": "XBB recombinant lineage defining mutations", | ||
| "sources": [ | ||
| ], | ||
| "type": "variant", | ||
| "variant": { | ||
| "Pango_lineages": [ | ||
| "XBB" | ||
| ], | ||
| "WHO_label": "Omicron", | ||
| "parent_lineage": "XBB-parent2", | ||
| "mrca_lineage": "XBB", | ||
| "lineage_name": "XBB", | ||
| "representative_genome": "" | ||
| }, | ||
| "tags": [ | ||
| "XBB" | ||
| ], | ||
| "note": "Unique mutations for XBB sublineage", | ||
| "sites": [ | ||
| "spike:V83A", | ||
| "spike:Y144-", | ||
| "spike:H146Q", | ||
| "spike:Q183E", | ||
| "spike:V213E", | ||
| "spike:R346T", | ||
| "spike:L368I", | ||
| "spike:V445P", | ||
| "spike:F486S", | ||
| "spike:F490S", | ||
|
|
||
| "nuc:C15738T", | ||
| "nuc:T15939C", | ||
| "nuc:T17859C" | ||
| ], | ||
| "rules": { | ||
| "min_alt": 5, | ||
| "max_ref": 3 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -30,7 +30,7 @@ | |
| "nuc:C14599T" | ||
| ], | ||
| "rules": { | ||
| "min_alt": 2, | ||
| "min_alt": 3, | ||
| "max_ref": 0 | ||
| } | ||
| } | ||