diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index ae9d110fe..b264efd35 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -18,7 +18,7 @@ jobs:
         with:
           python-version: "3.9"
       - run: pip install cram nextstrain-augur
-      - run: cram --shell=/bin/bash tests/sanitize-metadata.t
+      - run: cram --shell=/bin/bash tests/sanitize-metadata.t tests/annotate_metadata_with_index.t
 
   docs:
     uses: nextstrain/.github/.github/workflows/docs-ci.yaml@master
diff --git a/scripts/annotate_metadata_with_index.py b/scripts/annotate_metadata_with_index.py
index d7a77b517..fd643dc87 100644
--- a/scripts/annotate_metadata_with_index.py
+++ b/scripts/annotate_metadata_with_index.py
@@ -18,6 +18,8 @@
     index = pd.read_csv(
         args.sequence_index,
         sep="\t",
+        dtype={"strain": "string"},
+        index_col="strain",
     ).drop(
         columns=["length"],
     )
@@ -25,15 +27,12 @@
     new_columns = {
         column: f"_{column}"
         for column in index.columns
-        if column != "strain"
     }
     index = index.rename(columns=new_columns)
 
-    metadata.merge(
+    metadata.join(
         index,
-        on="strain",
     ).to_csv(
         args.output,
         sep="\t",
-        index=False,
     )
diff --git a/tests/annotate_metadata_with_index.t b/tests/annotate_metadata_with_index.t
new file mode 100644
index 000000000..dbbc95dc5
--- /dev/null
+++ b/tests/annotate_metadata_with_index.t
@@ -0,0 +1,28 @@
+Test script to annotate metadata with sequence index.
+
+  $ pushd "$TESTDIR" > /dev/null
+
+Annotate metadata with an index where strains have numeric names.
+
+  $ python3 ../scripts/annotate_metadata_with_index.py \
+  >  --metadata numeric_strains/metadata.tsv \
+  >  --sequence-index numeric_strains/sequence_index.tsv \
+  >  --output "$TMP/metadata_with_index.tsv"
+  $ wc -l "$TMP/metadata_with_index.tsv"
+  \s*3 .* (re)
+
+  $ rm -f "$TMP/metadata_with_index.tsv"
+
+Annotate metadata with an index where metadata uses the "name" column for strain names.
+This should produce the same result as above, except with a "name" column in the output.
+
+  $ python3 ../scripts/annotate_metadata_with_index.py \
+  >  --metadata numeric_strains/metadata_by_name.tsv \
+  >  --sequence-index numeric_strains/sequence_index.tsv \
+  >  --output "$TMP/metadata_with_index.tsv"
+  $ wc -l "$TMP/metadata_with_index.tsv"
+  \s*3 .* (re)
+
+  $ rm -f "$TMP/metadata_with_index.tsv"
+
+  $ popd > /dev/null
diff --git a/tests/numeric_strains/metadata.tsv b/tests/numeric_strains/metadata.tsv
new file mode 100644
index 000000000..aaa159de0
--- /dev/null
+++ b/tests/numeric_strains/metadata.tsv
@@ -0,0 +1,3 @@
+strain	virus	gisaid_epi_isl	genbank_accession	date	region	country	division	location	region_exposure	country_exposure	division_exposure	segment	length	host	age	sex	originating_lab	submitting_lab	authors	url	title	date_submitted
+1	ncov	?	MT450922	2020-03-05	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29812	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT450922	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC05/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds	2020-05-11
+2	ncov	?	MT451684	2020-03-31	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29806	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT451684	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC1000/2020, complete genome	2020-05-11
diff --git a/tests/numeric_strains/metadata_by_name.tsv b/tests/numeric_strains/metadata_by_name.tsv
new file mode 100644
index 000000000..f6c721c83
--- /dev/null
+++ b/tests/numeric_strains/metadata_by_name.tsv
@@ -0,0 +1,3 @@
+name	virus	gisaid_epi_isl	genbank_accession	date	region	country	division	location	region_exposure	country_exposure	division_exposure	segment	length	host	age	sex	originating_lab	submitting_lab	authors	url	title	date_submitted
+1	ncov	?	MT450922	2020-03-05	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29812	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT450922	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC05/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds	2020-05-11
+2	ncov	?	MT451684	2020-03-31	Oceania	Australia	Victoria		Oceania	Australia	Victoria	genome	29806	Homo sapiens	?	?	?	?	Seemann et al	https://www.ncbi.nlm.nih.gov/nuccore/MT451684	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC1000/2020, complete genome	2020-05-11
diff --git a/tests/numeric_strains/sequence_index.tsv b/tests/numeric_strains/sequence_index.tsv
new file mode 100644
index 000000000..d90752eeb
--- /dev/null
+++ b/tests/numeric_strains/sequence_index.tsv
@@ -0,0 +1,3 @@
+strain	length	A	C	G	T	N	other_IUPAC	-	?	invalid_nucleotides
+1	29812	8825	5433	5812	9498	242	2	0	0	0
+2	29806	8876	5461	5849	9558	62	0	0	0	0