# RSV-A Reference Sequence Question

**URL:** <https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908>\
**Category:** General\
**Created:** [June 12, 2025, 10:06pm UTC](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908 "2025-06-12T22:06:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![T4R4](https://avatars.discourse-cdn.com/v4/letter/t/5e9695/32.png) [@T4R4](https://nextstrain.discourse.group/u/T4R4)\
**Post date:** [June 12, 2025, 10:06pm UTC](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908/1 "2025-06-12T22:06:52Z")

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Hello,

I noticed that the referenced RSV-A NCBI accession has been updated to the INSDC reference that differs slightly from the A/England/397/2017 reference used in the RSV-A Nextclade dataset. I was wondering if there are plans to update the Nextclade dataset to use the INSDC reference or if the current reference will continue to be used?

> <https://github.com/nextstrain/rsv/commit/b51bbed65efc0078d58eef93458085f35d41e617>

Thank you for your time.

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**Author:** ![ivan-aksamentov](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/ivan-aksamentov/32/80_2.png) [@ivan-aksamentov](https://nextstrain.discourse.group/u/ivan-aksamentov)\
**Post date:** [June 13, 2025, 11:41am UTC](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908/2 "2025-06-13T11:41:38Z")

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Hi Tara @T4R4,

Sorry for the confusion!

My understanding is that it’s only a documentation change, i.e. in the `README.md` file Theo added a link to the PP109421.1 (same sequence as EPI\_ISL\_412866), now that it’s avaialble in an open database, and now we can give a link to it, so that people can use it (GISAID EPI\_ISL\_\* data is restricted).

Previously the `README.md` provided a link to an open LR699737, which is almost the same as EPI\_ISL\_412866, but not quite, so it required some explanation. None of that is needed now that we have PP109421.1.

So there is no dataset change planned. It is based on EPI\_ISL\_412866 and continues to be. The changes to `README.md` will be released in the next version of a dataset, once we have some actual changes, because what’s in `README.md` is only a visual change.

I double checked just now that EPI\_ISL\_412866 and PP109421.1 are indeed the same sequences:

```bash
# Download both sequences
curl -fsSLo "PP109421.1.fasta" "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=PP109421.1&rettype=fasta&retmode=text"
curl -fsSLo "EPI_ISL_412866.fasta" "https://raw.githubusercontent.com/nextstrain/nextclade_data/refs/heads/master/data/nextstrain/rsv/a/EPI_ISL_412866/reference.fasta"

# Make file formatting consistent
seqkit seq EPI_ISL_412866.fasta -s -n -i -w 0 > f1.txt
seqkit seq PP109421.1.fasta -s -n -i -w 0 > f2.txt

# Compare
diff f1.txt f2.txt

```

Output:

```diff
1c1
< >EPI_ISL_412866
---
> >PP109421.1

```

i.e. they only differ in header.

Let us know if you noticed any other problems we might have missed.

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<div class="post-metadata">

**Author:** ![T4R4](https://avatars.discourse-cdn.com/v4/letter/t/5e9695/32.png) [@T4R4](https://nextstrain.discourse.group/u/T4R4)\
**Post date:** [June 13, 2025, 2:20pm UTC](https://nextstrain.discourse.group/t/rsv-a-reference-sequence-question/1908/3 "2025-06-13T14:20:10Z")

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Hi Ivan,

Thank you for your response! My apologies, I accidentally interpreted the commit in the opposite order as I was thinking it reflected the current read me on the Nextclade site.

That makes sense!

Thank you for your time,  
Tara