# SARS-CoV-2 Sequences from Wastewater sample

**URL:** <https://nextstrain.discourse.group/t/sars-cov-2-sequences-from-wastewater-sample/1179>\
**Category:** Help and Getting Started\
**Created:** [July 13, 2022, 1:54pm UTC](https://nextstrain.discourse.group/t/sars-cov-2-sequences-from-wastewater-sample/1179 "2022-07-13T13:54:09Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![Carlotta](https://avatars.discourse-cdn.com/v4/letter/c/898d66/32.png) [@Carlotta](https://nextstrain.discourse.group/u/Carlotta)\
**Post date:** [July 13, 2022, 1:54pm UTC](https://nextstrain.discourse.group/t/sars-cov-2-sequences-from-wastewater-sample/1179/1 "2022-07-13T13:54:09Z")

</div>

Hi, I have uploaded SARS-CoV-2 FASTA sequences derived from **wastewater** samples into GISAID. On Nextclade, I have filtered for Host-Environment, and I can see only 5 samples right now even if there are many more uploaded into GISAID and they are not the one we uploaded. Moreover I can’t see our submitting lab from the filter either. Is it possible to see the wastewater samples on nexclade? or at least the sample from our lab? Thank you very much for the amazing work you are doing.  
Carlotta Olivero

---

<div class="post-metadata">

**Author:** ![james](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/james/32/11_2.png) [@james](https://nextstrain.discourse.group/u/james)\
**Post date:** [July 13, 2022, 10:26pm UTC](https://nextstrain.discourse.group/t/sars-cov-2-sequences-from-wastewater-sample/1179/2 "2022-07-13T22:26:58Z")

</div>

Hi @Carlotta - due to the huge number of sequences on GISAID (many millions) we heavily subsample the data for our nextstrain datasets with the aim of providing a representative view into the pandemic. This subsampling considers time and location ([e.g.](https://github.com/nextstrain/ncov/blob/master/nextstrain_profiles/nextstrain-gisaid/builds.yaml#L173-L202)) and so I would expect few wastewater samples to be sampled. (Furthermore, there are multiple QC filters which wastewater samples may be more likely to fail?)

You could run a specific build with a sampling scheme focused on wastewater samples – the best starting point would be [this tutorial](https://docs.nextstrain.org/projects/ncov/en/stable/tutorial/intro.html) and don’t hesitate to post here if you get stuck.

P.S. If data from your lab is in a nextstrain dataset but the Submitting Lab / Originating Lab isn’t available as a filter then that’s a bug! Could you let us know the dataset + lab name & I’ll chase this up.

---

<div class="post-metadata">

**Author:** ![Carlotta](https://avatars.discourse-cdn.com/v4/letter/c/898d66/32.png) [@Carlotta](https://nextstrain.discourse.group/u/Carlotta)\
**Post date:** [July 14, 2022, 1:26pm UTC](https://nextstrain.discourse.group/t/sars-cov-2-sequences-from-wastewater-sample/1179/3 "2022-07-14T13:26:20Z")

</div>

> [@james](#):
>
> onsiders time and location

Thank you very much for this exaustive explanation. I will try to follow the tutorial!

As per the Submitting Lab / Originating Lab, the datasets I have uploaded on GISAID are for example EPI\_ISL\_13699833 (hCoV-19/env/Italy/PIE-ARPA-22BL10879/2022) and EPI\_ISL\_12751712 (hCoV-19/env/Italy/PIE-ARPA-22BL10880/2022). Can you see the submitting lab from there?

Many thanks for the help!