diff --git a/defaults/include.txt b/defaults/include.txt
index 91f5039ad..3d7a12350 100644
--- a/defaults/include.txt
+++ b/defaults/include.txt
@@ -1,3 +1,2 @@
 Wuhan/Hu-1/2019
 Wuhan-Hu-1/2019
-Wuhan/WH01/2019
diff --git a/defaults/parameters.yaml b/defaults/parameters.yaml
index 2369f9f50..188077039 100644
--- a/defaults/parameters.yaml
+++ b/defaults/parameters.yaml
@@ -89,8 +89,12 @@ filter:
 # will help reduce the number of genetically identical strains that get chosen,
 # and allows for more diversity represented on the tree.
 priorities:
+  ignore_sequences:
+    - Wuhan/Hu-1/2019
+    - Wuhan-Hu-1/2019
   crowding_penalty: 0.1
 
+
 # Alignment settings
 # Alignments are partitioned into smaller groups to speed up the overall alignment process.
 # The number of sequences per group determines the run time of a single alignment job.
diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
index ca546c63c..975de94c2 100644
--- a/workflow/snakemake_rules/main_workflow.smk
+++ b/workflow/snakemake_rules/main_workflow.smk
@@ -369,7 +369,7 @@ rule proximity_score:
         "benchmarks/proximity_score_{build_name}_{focus}.txt"
     params:
         chunk_size=10000,
-        ignore_seqs = config['refine']['root']
+        ignore_seqs = config['priorities']['ignore_sequences'],
     resources:
         # Memory scales at ~0.15 MB * chunk_size (e.g., 0.15 MB * 10000 = 1.5GB).
         mem_mb=4000