# Date confidence, ORF1a of Sarbecovirus, 104 genomes

**URL:** <https://nextstrain.discourse.group/t/date-confidence-orf1a-of-sarbecovirus-104-genomes/554>\
**Category:** Uncategorized\
**Created:** [May 31, 2021, 11:17pm UTC](https://nextstrain.discourse.group/t/date-confidence-orf1a-of-sarbecovirus-104-genomes/554 "2021-05-31T23:17:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![babarlelephant](https://avatars.discourse-cdn.com/v4/letter/b/8e8cbc/32.png) [@babarlelephant](https://nextstrain.discourse.group/u/babarlelephant)\
**Post date:** [May 31, 2021, 11:17pm UTC](https://nextstrain.discourse.group/t/date-confidence-orf1a-of-sarbecovirus-104-genomes/554/1 "2021-05-31T23:17:18Z")

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Hi, all the metadata is filled (including precise locations for most sequences) [http://babarlelephant.free-hoster.net/dist/index\_sarbecovirus-1000-12000.html?c=clade\_membership&ci&p=full&r=division&transmissions=hide](http://babarlelephant.free-hoster.net/dist/index_sarbecovirus-1000-12000.html?c=clade_membership&ci&p=full&r=division&transmissions=hide)

ORF1a is easier to align, not many recombinations, the substitution rate is mostly uniform and not too low, and PrC31 becomes very close to SARS-CoV-2.

The clock rate was estimated by comparing the ORF1a SNP of the May 2021 SARS-CoV-2 sequences with Wuhan-Hu-1, obtaining 0.0005438subs/site/year.

The confidence intervals given by Treetime are very tight, I wonder if this is true or if I chose a wrong param.

My other question, is it possible to upload the json, fasta, metadata and Snakemake to nextstrain/community?

Thanks a lot.

```auto
rule refine:
    message:
        """
        Refining tree
          - estimate timetree
          - use {params.coalescent} coalescent timescale
          - estimate {params.date_inference} node dates
        """
    input:
        tree = rules.tree.output.tree,
        alignment = rules.align.output,
        metadata = input_metadata
    output:
        tree = "results/tree.nwk",
        node_data = "results/branch_lengths.json"
    params:
        coalescent = "opt",
        date_inference = "marginal",
        root = "internal-node-root",
        clock_rate = 0.0005438
    shell:
        """
        augur refine \
            --tree {input.tree} \
            --alignment {input.alignment} \
            --metadata {input.metadata} \
            --output-tree {output.tree} \
            --output-node-data {output.node_data} \
            --coalescent {params.coalescent} \
			--timetree \
            --date-inference {params.date_inference} \
            --date-confidence \
            --keep-polytomies \
            --precision 1 \
            --clock-rate {params.clock_rate}
        """

```

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<div class="post-metadata">

**Author:** ![babarlelephant](https://avatars.discourse-cdn.com/v4/letter/b/8e8cbc/32.png) [@babarlelephant](https://nextstrain.discourse.group/u/babarlelephant)\
**Post date:** [June 2, 2021, 2:51am UTC](https://nextstrain.discourse.group/t/date-confidence-orf1a-of-sarbecovirus-104-genomes/554/2 "2021-06-02T02:51:23Z")

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Beast (same alignement and fixed clock rate) agrees with treetime

 ![sarbecovirus-1000-12000_with_dates..MCMC.trees](https://canada1.discourse-cdn.com/flex031/uploads/nextstrain/original/1X/0418a045befa3fe723b7f9dc8a3b9fdac6854520.jpeg)

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**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [June 10, 2021, 12:21pm UTC](https://nextstrain.discourse.group/t/date-confidence-orf1a-of-sarbecovirus-104-genomes/554/3 "2021-06-10T12:21:36Z")

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My take here is that model mispecification and time dependent rates of evolution will render this extrapolation pretty meaningless. Doing the same with HIV gives results that are orders of magnitude off. I would not read much into it.