Potential BA.5.2 sublineage with ORF3a:T14I (821 seqs as of 2022-09-17; Australia, Asia, North America, Europe)

[alurqu]

There may be a BA.5.2 sublineage with ORF3a:T14I (C25433T) with the first known detection in New South Wales, Australia with detected spread to Asia, North America, and Europe. Note that detections in Indonesia and Thailand occurred very soon after the detection in New South Wales.

Also note that ORF3a:T14I (C25433T) was one of the defining mutations for AY.43.1 (see the designation comment on Issue 319).

As of 2022-08-08, Cov-Spectrum reports 174 BA.5.2+ORF3a:14I sequences:

Source: https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?variantQuery=nextcladePangoLineage%3ABA.5.2+%26+ORF3a%3AT14I&

Growth estimates are early and may be high, but here are the current Cov-Spectrum estimates as of 2022-08-08:

Cov-Spectrum calculates a growth advantage of 48% compared to BA.5.2* in the United States:

Source: https://cov-spectrum.org/explore/United%20States/AllSamples/AllTimes/variants?variantQuery=nextcladePangoLineage%3ABA.5.2*&variantQuery1=nextcladePangoLineage%3ABA.5.2+%26+ORF3a%3AT14I&analysisMode=CompareToBaseline&

Cov-Spectrum calculates a growth advantage of 56% compared to BA.5* in the United States:
@BA.5 Growth image@
Source: https://cov-spectrum.org/explore/United%20States/AllSamples/AllTimes/variants?variantQuery=nextcladePangoLineage%3ABA.5*&variantQuery1=nextcladePangoLineage%3ABA.5.2+%26+ORF3a%3AT14I&analysisMode=CompareToBaseline&

As of 2022-08-08, UShER shows all of the GenBank samples are on a single subtree:

To visualize on UShER: https://nextstrain.org/fetch/github.com/alurqu/pango-designation-support-alurqu/raw/main/subtreeAuspice1_genome_BA.5.2%2BORF3a_14I.json

First Outbreak.info sequences: New South Wales, Australia 2022-06-13; Indonesia, 2022-06-14; Thailand, 2022-06-15

First GenBank sequence: Florida, USA 2022-06-17

Most Recent GenBank sequence: Connecticut, USA 2022-08-01

A zip archive of GenBank-formatted and derived metadata and FASTA files plus UShER output files for these sequences is available at
Support_BA.5.2+ORF3a_14I.zip

The Outbreak.info link for this potential lineage is https://outbreak.info/situation-reports?pango=BA.5.2&muts=ORF3a%3AT14I&loc=USA&loc=GBR&loc=AUS&loc=IDN&loc=KOR&loc=SGP&loc=EST&loc=THA&loc=ISR&loc=DNK&loc=JPN&loc=ITA&loc=FRA&selected=Worldwide&overlay=false.

[FedeGueli]

191 seqs on covspectrum as today

[alurqu]

As of 2022-08-24, South Korea has reported 103 sequences of BA.5.2+ORF3a:T41I and has the most occurrences of this potential sublineage.

[FedeGueli]

337 seqs as today on Usher. fast growing one:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1900a_7331d0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C25433T

Gisaid query: NS3_T14I, NSP13_T127N

[corneliusroemer]

Not sure this is doing much - lets monitor further

[FedeGueli]

424 sequences on Gisaid ( query : NS3_T14I,NSP13 T127N)

, it should be added that this likely originated in Indonesia , where it represents 39 out of 7064 samples after 14th of June

@corneliusroemer in the list of the proposed still undesignated lineages it is the 4th ordering it for Low CI of Growth Advantage and the one with more sequences in the first 4
(VS BA.5.2 )
https://cov-spectrum.org/collections/23

So to me it is clearly doing something and it should be designated.
.

[FedeGueli]

533 virus on Gisaid as today
10 newly updated from SouthKorea (tot 156seqs from SK) some of them travel related with south east asia,
13 newly updated from Japan (43 tot) 2 related with travel with South Korea.

I think the high proportion of this sublineage detected in South Korea representing around 2% of samples collected there in August (56/3091) could make it deserving a designation beyond its growth advantage . @corneliusroemer @InfrPopGen @aq-sun @chrisruis

[FedeGueli]

Eventually it could be decided if @alurqu agree to designate it starting with an additional Orf1a:D2026A: Gisaid query NSP3_D1208A,NS3_T14I,NSP13_T127N intercepts 298 sequences of this sub sublineage of which the half coming from South Korea (153 seqs).
This represents quite 100% of South Korean sequences of this sublineage (153/156)

Interesting designating this starting with Orf1a:D2026A got also the most of Japanese sequences (31) which cluster together in a well defined branch with an additonal spike mutation:S:H1083Y

and an Indonesian Australian cluster defined by orf1a:L2778F

Here the bigger picture:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_7787_71bc0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C8597T

@alurqu @corneliusroemer if you have time take a look at my proposal consisting in:

1. Designating this lineage starting deeper in the tree with Orf1a:D2026A

2. Designating the Japanese cluster clearly corresponding with S:H1083Y

3. Monitoring if the Orf1a:l2778F cluster grows

[alurqu]

@FedeGueli Ultimately how and even if this lineage gets designated is not in my control. That is the scope of the Lineage Designation Committee (LDC). My only role is to humbly call the LDC's attention to lineages that may need to be designated.

With that said, I'll note that McGrath et al https://doi.org/10.1073/pnas.2204717119 found that deletions of ORF3a/b attenuated SARS-CoV-2 even in interferon-incompetent cells, so to me it seems plausible that the ORF3a:T14I mutation may have changed the fitness of the virus.

It could be reasonable to grant BA.5.2+ORF3a:T14I a lineage designation and possibly grant the branches you mentioned designation as sublineages. Or perhaps the LDC would prefer to go straight to designating the sublineages. I will leave that to the wisdom of the LDC.

[corneliusroemer]

Ah this is on the ORF1b:1050N branch - ok I'll designate to reduce number of unspecified BA.5.2 on that branch

[FedeGueli]

Nice this ome got a name. it is quite fast among the lineages without 346/444/460 so being quite big it could have opportunity to acquire one of them and jump to high rankings.