diff --git a/scripts/annotate_metadata_with_index.py b/scripts/annotate_metadata_with_index.py
index d7a77b517..79d173d5d 100644
--- a/scripts/annotate_metadata_with_index.py
+++ b/scripts/annotate_metadata_with_index.py
@@ -18,6 +18,7 @@
     index = pd.read_csv(
         args.sequence_index,
         sep="\t",
+        dtype={"strain": "string"}
     ).drop(
         columns=["length"],
     )