Updates Flu Antiviral Resistance Detection Documentation (#758)

* updated list of flu drugs in docs * added mutation explanations table * switched "mutation" to "aa_substitution" for clarity * updated flu docs with link to explanations table * added task file to antiviral subs links table * added publication link to antiviral subs links table * fix theiacov path --------- Co-authored-by: Sage Wright <[email protected]>
theiagen · Feb 14, 2025 · a610dc8 · a610dc8
1 parent 27db5cf
commit a610dc8
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/docs/assets/files/antiviral_resistance_flu_aa_substitutions_explanations.xlsx b/docs/assets/files/antiviral_resistance_flu_aa_substitutions_explanations.xlsx
diff --git a/docs/workflows/genomic_characterization/theiacov.md b/docs/workflows/genomic_characterization/theiacov.md
@@ -1009,12 +1009,15 @@ All input reads are processed through "core tasks" in the TheiaCoV Illumina, ONT
 
     This sub-workflow determines which, if any, antiviral mutations are present in the sample. 
 
-    The assembled HA, NA, PA, PB1 and PB2 segments are compared against [a list of known amino-acid substitutions associated with resistance](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/gene_typing/drug_resistance/task_flu_antiviral_subs.wdl) to the antivirals  A_315675, compound_367, Favipiravir, Fludase, L_742_001, Laninamivir, Oseltamivir (tamiflu), Peramivir, Pimodivir, Xofluza, and Zanamivir. The list of known antiviral amino acid substitutions can be expanded via optional user input `antiviral_aa_subs` in the format "`NA:V95A,HA:I97V`", i.e. `Protein:AAPositionAA`. 
+    The assembled HA, NA, PA, PB1 and PB2 segments are compared against [a list of known amino-acid substitutions associated with resistance](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/gene_typing/drug_resistance/task_flu_antiviral_subs.wdl) to the antivirals  A_315675, Amantadine, compound_367, Favipiravir, Fludase, L_742_001, Laninamivir, Oseltamivir (tamiflu), Peramivir, Pimodivir, Rimantadine, Xofluza, and Zanamivir. The list of known amino-acid substitutions associated with resistance can be expanded via optional user input `antiviral_aa_subs` in the format "`NA:V95A,HA:I97V`", i.e. `Protein:AAPositionAA`. 
+    The list of amino-acid substitutions associated with antiviral resistance includes both substitutions reported to confer antiviral resistance in the scientific literature and those inferred to potentially cause antiviral resistance based on an analogous mutation reported to confer antiviral resistance in another flu subtype. A table with the explanation for each amino-acid substitution in the antiviral resistance task is available [here](../../assets/files/antiviral_resistance_flu_aa_substitutions_explanations.xlsx).
 
     !!! techdetails "Antiviral Substitutions Technical Details"        
         |  | Links |
         | --- | --- |
         | Workflow | [wf_influenza_antiviral_substitutions.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_influenza_antiviral_substitutions.wdl) |
+        | Task | [task_flu_antiviral_subs.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/main/tasks/gene_typing/drug_resistance/task_flu_antiviral_subs.wdl) |
+        | Publication | [Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza](https://doi.org/10.1016/j.tibtech.2019.09.009)
 
 ??? task "`genoflu`"