# Twice-mutated locations between parent and child lineages

**URL:** <https://nextstrain.discourse.group/t/twice-mutated-locations-between-parent-and-child-lineages/1372>\
**Category:** Help and Getting Started\
**Created:** [April 30, 2023, 3:38pm UTC](https://nextstrain.discourse.group/t/twice-mutated-locations-between-parent-and-child-lineages/1372 "2023-04-30T15:38:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ciscorucinski](https://avatars.discourse-cdn.com/v4/letter/c/67e7ee/32.png) [@ciscorucinski](https://nextstrain.discourse.group/u/ciscorucinski)\
**Post date:** [April 30, 2023, 3:38pm UTC](https://nextstrain.discourse.group/t/twice-mutated-locations-between-parent-and-child-lineages/1372/1 "2023-04-30T15:38:49Z")

</div>

I have been working with data that is generated over at [GitHub - corneliusroemer/pango-sequences: Consensus sequences for each Pango lineage](https://github.com/corneliusroemer/pango-sequences). So CC @corneliusroemer

Since the documentation states the following, I thought I would give this forum a try.

> The sequences contained here are the ones used in Nextclade reference trees and produced by code contained in the nextclade\_data\_workflows/sars-cov-2 repository.

Within the `Caveats` documentation, it states the following

> - Currently, when one position is mutated twice, e.g. `486F->S->L` this gives rise to both a reversion and a new substitution. This might be changed in the future.

Well, I have been able to locate all of these twice mutated lineages, and I am wondering how to go about processing these special cases.

I am a novice when it comes to using the nextStrain UI. I have noticed that a large portion of these twice-mutated lineages don’t seem searchable, so I can’t verify those. I have been able to find a few lineages within NextStrain, and it seems like the Reversion is ignored and the substitution is accepted (i.e. B.1.617.2). `XBB.1.5` is also a lineage that has twice-mutated positions. I have been trying to figure out how to view the mutations for just `XBB.1.5` and not one of the individual 261 sequences of `XBB.1.5`

Based on the documentation, dropping the duplicated reversions does seem to be a reasonable assumption to do for all these twice-mutated lineages.

> … The algorithm used to create these sequences has a high threshold to allow reversions, almost all sequences need to be reverted, otherwise it’s assumed the reversions are an artefact.

**So I am wondering if there are valid twice-mutated locations and what that actually means for what happened.** I get the general idea as stated in the documentation (486F-\>S-\>L). But a lot of questions and confusion for how that can happen.

I have some sample output from my processing of the data at [GitHub - corneliusroemer/pango-sequences: Consensus sequences for each Pango lineage](https://github.com/corneliusroemer/pango-sequences).

## Output

### XBB.1.5

Here is data for `XBB.1.5` and it’s parent lineage `XBB.1`. There are several `XBB.1.5` sublineages that also have this twice-mutated positions.

For nucleotide position 1, there have been 2 nucleotide mutations.

- One Reversion `A1G`
- One Substitution `A1T`.

```python
Looking at variant: XBB.1.5

	PARENT (XBB.1)
	(1) PARENT ALL MUTS : {'S:S373P', 'S:G252V', 'C25584T', 'T27384C', '29734-29758', 'A18163G', 'ORF1a:K47R', 'T21810C', 'S:Y505H', 'S:N969K', 'C23525T', 'N:E31-', 'ORF1a:P3395H', 'S:Q183E', '21633-21641', 'S:P26-', 'C241T', 'A24424T', '28362-28370', 'S:R346T', 'A22688G', 'S:D614G', 'C23854A', 'ORF1a:F3677-', 'S:T478K', 'A23013C', 'S:F486S', 'C27807T', 'C17410T', 'T16342C', 'G22813T', 'ORF9b:P10S', 'E:T9I', 'C21618T', 'C26858T', 'T22679C', 'ORF9b:A29-', 'C15738T', 'C26270T', 'ORF3a:T223I', 'S:S477N', 'S:S375F', 'A29510C', 'C23604A', 'G28883C', 'G22992A', 'A22786C', 'A23403G', 'ORF1a:G1307S', 'C14408T', 'M:Q19E', 'S:T19I', 'S:N440K', 'S:D405N', 'G4184A', 'C12880T', 'S:N679K', 'C3037T', 'C9866T', 'S:Q954H', 'C25416T', 'S:H146Q', 'S:G446S', 'G22317T', 'G28881A', 'ORF9b:E27-', 'N:R203K', 'G22578A', 'ORF1b:R1315C', 'C19955T', 'T15939C', 'S:N764K', 'S:L24-', 'A27259C', 'C9344T', 'S:L368I', 'C22674T', 'ORF1a:L3201F', 'S:R408S', 'C9534T', 'S:K417N', 'S:A27S', 'S:Q498R', 'ORF1a:T842I', 'ORF9b:N28-', 'T22200A', 'ORF1a:T3090I', 'G21987A', 'S:Y144-', 'C22686T', 'T17859C', 'S:N501Y', 'G10447A', 'S:G142D', 'S:N460K', 'C15714T', 'ORF6:D61L', 'N:R32-', 'S:D796Y', 'G22895C', 'N:P13L', 'G22898A', 'E:T11A', 'ORF1a:L3027F', 'C22995A', 'C10449A', 'ORF1b:S959P', 'T23031C', 'S:T376A', 'S:P25-', 'G26709A', 'A20055G', 'C2790T', 'C26577G', 'C22664A', 'G23948T', 'C10198T', 'G28882A', 'C22109G', 'A405G', 'A1G', 'T22942G', 'A28271T', 'S:E484A', 'M:A63T', 'A23055G', 'G15451A', 'G27382C', 'N:S33-', 'S:S371F', 'ORF1a:G3676-', 'G22577C', 'ORF1a:S3675-', 'ORF1b:P314L', 'C28311T', 'C25000T', 'C44T', 'C4321T', 'N:G204R', '11288-11296', 'T23019C', 'C22000A', 'T23599G', 'A19326G', 'S:V445P', 'S:V213E', 'G22775A', 'C26060T', 'T22882G', 'ORF1b:T2163I', 'T24469A', 'ORF1a:S135R', 'S:G339H', 'A9424G', 'A27383T', 'ORF1a:T3255I', 'S:H655Y', 'G22599C', 'T23075C', 'A26275G', 'S:V83A', 'T22896C', 'ORF1b:G662S', 'S:F490S', 'A23063T', 'ORF1b:I1566V', 'N:S413R', 'T670G', 'C10029T', 'S:P681H', '21992-21994'}

	VARIANT (XBB.1.5)
	(2) ALL NEW MUTS : {'T23018C', 'S:F486P', '29734-29759', 'ORF8:G8*', 'A1T', 'G27915T'}
	(3) NUC REVERSIONS ONLY : {'A1G', '29734-29758'}

	INTERSECTION (1) ∩ (3) : {'A1G', '29734-29758'}

	NUC NEW SUBSTITUTION : {'T23018C', 'A1T', 'G27915T'}
	NUC ALL REVERSIONS : {'A1G', '29734-29758'}
	DUP LOCATIONS (2) & (3) : ['nucleotide substitution: Root[A 1 T] Parent[? 1 T]', 'nucleotide substitution: Root[A 1 G] Parent[? 1 G]']

```

### Subset of other XBB.1.5 sublineages

```python
Looking at variant: XBB.1.5.27

	PARENT (XBB.1.5)
	(1) PARENT ALL MUTS : {'S:S373P', 'S:G252V', 'C25584T', 'T27384C', 'A18163G', 'ORF1a:K47R', 'T21810C', 'S:Y505H', 'S:N969K', 'C23525T', 'N:E31-', 'ORF1a:P3395H', 'S:Q183E', '21633-21641', 'S:P26-', 'C241T', 'A24424T', '28362-28370', 'S:R346T', 'ORF8:G8*', 'A22688G', 'S:D614G', 'C23854A', 'ORF1a:F3677-', 'S:T478K', 'A23013C', 'C27807T', 'C17410T', 'T16342C', 'G22813T', 'ORF9b:P10S', 'E:T9I', 'C21618T', 'C26858T', 'T22679C', 'ORF9b:A29-', 'C15738T', 'C26270T', 'ORF3a:T223I', 'S:S477N', 'S:S375F', 'A29510C', 'C23604A', 'G28883C', 'G22992A', 'A22786C', 'A23403G', 'ORF1a:G1307S', 'C14408T', 'M:Q19E', 'S:T19I', 'S:N440K', 'S:D405N', 'G4184A', 'C12880T', 'S:N679K', 'C3037T', 'C9866T', 'S:Q954H', 'C25416T', 'S:H146Q', 'S:G446S', 'G22317T', 'G28881A', 'ORF9b:E27-', 'N:R203K', 'G22578A', 'ORF1b:R1315C', 'C19955T', 'T15939C', 'S:N764K', 'S:L24-', 'A27259C', 'C9344T', 'S:L368I', 'C22674T', 'ORF1a:L3201F', 'S:R408S', 'C9534T', 'S:K417N', 'S:A27S', 'S:Q498R', 'ORF1a:T842I', 'ORF9b:N28-', 'T22200A', 'ORF1a:T3090I', 'G21987A', 'G27915T', 'S:Y144-', 'C22686T', 'T17859C', 'S:N501Y', 'G10447A', 'S:G142D', 'S:N460K', '29734-29759', 'C15714T', 'ORF6:D61L', 'N:R32-', 'S:D796Y', 'G22895C', 'N:P13L', 'G22898A', 'E:T11A', 'ORF1a:L3027F', 'C22995A', 'C10449A', 'ORF1b:S959P', 'T23031C', 'S:T376A', 'S:P25-', 'G26709A', 'A20055G', 'C2790T', 'C26577G', 'C22664A', 'G23948T', 'C10198T', 'G28882A', 'C22109G', 'A405G', 'T22942G', 'A28271T', 'S:E484A', 'M:A63T', 'A23055G', 'G15451A', 'G27382C', 'N:S33-', 'S:S371F', 'ORF1a:G3676-', 'G22577C', 'ORF1a:S3675-', 'ORF1b:P314L', 'C28311T', 'C25000T', 'C44T', 'C4321T', 'N:G204R', '11288-11296', 'T23019C', 'C22000A', 'T23599G', 'A19326G', 'S:V445P', 'S:V213E', 'G22775A', 'C26060T', 'T22882G', 'ORF1b:T2163I', 'T24469A', 'ORF1a:S135R', 'S:G339H', 'A9424G', 'A27383T', 'ORF1a:T3255I', 'S:H655Y', 'G22599C', 'T23075C', 'A26275G', 'T23018C', 'S:F486P', 'S:V83A', 'T22896C', 'ORF1b:G662S', 'S:F490S', 'A23063T', 'ORF1b:I1566V', 'N:S413R', 'T670G', 'C10029T', 'S:P681H', 'A1T', '21992-21994'}

	VARIANT (XBB.1.5.27)
	(2) ALL NEW MUTS : {'T10204C', 'S:T478R', 'T17124C', 'C22995G', 'T11431C', 'ORF1a:E1015G', 'A3309G'}
	(3) NUC REVERSIONS ONLY : {'C22995A'}

	INTERSECTION (1) ∩ (3) : {'C22995A'}

	NUC NEW SUBSTITUTION : {'T10204C', 'T17124C', 'C22995G', 'T11431C', 'A3309G'}
	NUC ALL REVERSIONS : {'C22995A'}
	DUP LOCATIONS (2) & (3) : ['nucleotide substitution: Root[C 22995 G] Parent[? 22995 G]', 'nucleotide substitution: Root[C 22995 A] Parent[? 22995 A]']

Looking at variant: XBB.1.5.28

	PARENT (XBB.1.5)
	(1) PARENT ALL MUTS : {'S:S373P', 'S:G252V', 'C25584T', 'T27384C', 'A18163G', 'ORF1a:K47R', 'T21810C', 'S:Y505H', 'S:N969K', 'C23525T', 'N:E31-', 'ORF1a:P3395H', 'S:Q183E', '21633-21641', 'S:P26-', 'C241T', 'A24424T', '28362-28370', 'S:R346T', 'ORF8:G8*', 'A22688G', 'S:D614G', 'C23854A', 'ORF1a:F3677-', 'S:T478K', 'A23013C', 'C27807T', 'C17410T', 'T16342C', 'G22813T', 'ORF9b:P10S', 'E:T9I', 'C21618T', 'C26858T', 'T22679C', 'ORF9b:A29-', 'C15738T', 'C26270T', 'ORF3a:T223I', 'S:S477N', 'S:S375F', 'A29510C', 'C23604A', 'G28883C', 'G22992A', 'A22786C', 'A23403G', 'ORF1a:G1307S', 'C14408T', 'M:Q19E', 'S:T19I', 'S:N440K', 'S:D405N', 'G4184A', 'C12880T', 'S:N679K', 'C3037T', 'C9866T', 'S:Q954H', 'C25416T', 'S:H146Q', 'S:G446S', 'G22317T', 'G28881A', 'ORF9b:E27-', 'N:R203K', 'G22578A', 'ORF1b:R1315C', 'C19955T', 'T15939C', 'S:N764K', 'S:L24-', 'A27259C', 'C9344T', 'S:L368I', 'C22674T', 'ORF1a:L3201F', 'S:R408S', 'C9534T', 'S:K417N', 'S:A27S', 'S:Q498R', 'ORF1a:T842I', 'ORF9b:N28-', 'T22200A', 'ORF1a:T3090I', 'G21987A', 'G27915T', 'S:Y144-', 'C22686T', 'T17859C', 'S:N501Y', 'G10447A', 'S:G142D', 'S:N460K', '29734-29759', 'C15714T', 'ORF6:D61L', 'N:R32-', 'S:D796Y', 'G22895C', 'N:P13L', 'G22898A', 'E:T11A', 'ORF1a:L3027F', 'C22995A', 'C10449A', 'ORF1b:S959P', 'T23031C', 'S:T376A', 'S:P25-', 'G26709A', 'A20055G', 'C2790T', 'C26577G', 'C22664A', 'G23948T', 'C10198T', 'G28882A', 'C22109G', 'A405G', 'T22942G', 'A28271T', 'S:E484A', 'M:A63T', 'A23055G', 'G15451A', 'G27382C', 'N:S33-', 'S:S371F', 'ORF1a:G3676-', 'G22577C', 'ORF1a:S3675-', 'ORF1b:P314L', 'C28311T', 'C25000T', 'C44T', 'C4321T', 'N:G204R', '11288-11296', 'T23019C', 'C22000A', 'T23599G', 'A19326G', 'S:V445P', 'S:V213E', 'G22775A', 'C26060T', 'T22882G', 'ORF1b:T2163I', 'T24469A', 'ORF1a:S135R', 'S:G339H', 'A9424G', 'A27383T', 'ORF1a:T3255I', 'S:H655Y', 'G22599C', 'T23075C', 'A26275G', 'T23018C', 'S:F486P', 'S:V83A', 'T22896C', 'ORF1b:G662S', 'S:F490S', 'A23063T', 'ORF1b:I1566V', 'N:S413R', 'T670G', 'C10029T', 'S:P681H', 'A1T', '21992-21994'}

	VARIANT (XBB.1.5.28)
	(2) ALL NEW MUTS : {'T17124C', 'C22995G', 'S:T478R'}
	(3) NUC REVERSIONS ONLY : {'C22995A'}

	INTERSECTION (1) ∩ (3) : {'C22995A'}

	NUC NEW SUBSTITUTION : {'T17124C', 'C22995G'}
	NUC ALL REVERSIONS : {'C22995A'}
	DUP LOCATIONS (2) & (3) : ['nucleotide substitution: Root[C 22995 G] Parent[? 22995 G]', 'nucleotide substitution: Root[C 22995 A] Parent[? 22995 A]']

```

---

<div class="post-metadata">

**Author:** ![ciscorucinski](https://avatars.discourse-cdn.com/v4/letter/c/67e7ee/32.png) [@ciscorucinski](https://nextstrain.discourse.group/u/ciscorucinski)\
**Post date:** [April 30, 2023, 4:12pm UTC](https://nextstrain.discourse.group/t/twice-mutated-locations-between-parent-and-child-lineages/1372/2 "2023-04-30T16:12:41Z")

</div>

Finally re-found the link to specific variants [https://nextstrain.org/staging/nextclade/sars-cov-2/?s=XBB.1.5](https://nextstrain.org/staging/nextclade/sars-cov-2/?s=XBB.1.5)

Yeah, so even for XBB.1.5, the reversion is not what is listed