diff --git a/CHANGES.md b/CHANGES.md
index 0f8033abc..9e0e1a1ec 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -2,6 +2,11 @@
 
 ## __NEXT__
 
+### Bug Fixes
+
+* filter: Improve speed of checking duplicates in metadata, especially for large files. [#1466][] (@victorlin)
+
+[#1466]: https://github.com/nextstrain/augur/pull/1466
 
 ## 24.4.0 (15 May 2024)
 
diff --git a/augur/filter/_run.py b/augur/filter/_run.py
index 9a82c7f00..682ff46dc 100644
--- a/augur/filter/_run.py
+++ b/augur/filter/_run.py
@@ -180,7 +180,7 @@ def run(args):
     for metadata in metadata_reader:
         duplicate_strains = (
             set(metadata.index[metadata.index.duplicated()]) |
-            set(metadata.index[metadata.index.isin(metadata_strains)])
+            (set(metadata.index) & metadata_strains)
         )
         if len(duplicate_strains) > 0:
             cleanup_outputs(args)