diff --git a/nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk b/nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk
index 23a38ee8d..01be8ad67 100644
--- a/nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk
+++ b/nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk
@@ -92,7 +92,8 @@ rule gisaid_21L_aligned:
         exec 2> {log:q}
 
         < {input.references:q} \
-          zstd \
+          seqkit grep --by-name --pattern 21L \
+        | zstd \
         > {output.aligned}
 
         < {input.aligned:q} \