Potential BA.5.1 sublineage with ORF1a:I2368T and ORF1a:Q3922R (Mostly Denmark; 324 seqs as of 2022-08-03)

[alurqu]

There may be a BA.5.1 sublineage with ORF1a:I2368T (T7368C), ORF1a:Q3922R (A12030G), and also possibly synonymous mutation T6376C first detected in Switzerland and sampled most often in Denmark.

As of 2022-08-03, Cov-Spectrum reports 324 BA.5.1+ORF1a:2368T+ORF1a:3922R sequences:

Source: https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?variantQuery=nextcladePangoLineage%3ABA.5.1+%26+ORF1a%3AI2368T+%26+ORF1a%3AQ3922R&

As of 2022-08-03, Cov-Spectrum calculates a growth advantage of 87% compared to BA.5.1* in Europe:

Source: https://cov-spectrum.org/explore/Europe/AllSamples/AllTimes/variants?variantQuery=nextcladePangoLineage%3ABA.5.1*&variantQuery1=nextcladePangoLineage%3ABA.5.1+%26+ORF1a%3AI2368T+%26+ORF1a%3AQ3922R&analysisMode=CompareToBaseline&

Note; As of 2022-08-03, Cov-Spectrum reports an inability to determine the growth advantage in Denmark where this potential sublineage has been observed most frequently. Also, the Cov-Spectrum growth advantage calculation may be an over-estimate especially considering the absence of Spike mutations, but as of this writing this growth advantage is what Cov-Spectrum calculates.

As of 2022-08-03, 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.5.1%2BORF1a_2368T%2BORF1a_3922R.json

First GenBank sequence: Switzerland 2022-05-28

Most Recent GenBank sequence: Hovedstaden, Denmark 2022-07-11

A zip archive of GenBank-formatted and derived metadata and FASTA files plus UShER output files for these sequences is available at
Support_BA.5.1+ORF1a_2368T+ORF1a_3922R.zip

The Outbreak.info link for this potential lineage is https://outbreak.info/situation-reports?pango=BA.5.1&muts=ORF1a%3AI2368T&muts=ORF1a%3AQ3922R.

[silcn]

Note; As of 2022-08-03, Cov-Spectrum reports an inability to determine the growth advantage in Denmark where this potential sublineage has been observed most frequently. Also, the Cov-Spectrum growth advantage calculation may be an over-estimate especially considering the absence of Spike mutations, but as of this writing this growth advantage is what Cov-Spectrum calculates.

I'm getting a growth advantage of 48% in Denmark over the last two months, but it looks like the classic cluster/superspreading effect - a big increase followed by a plateau. So I wouldn't expect the advantage to be sustained.

[FedeGueli]

Agree with @silcn Denmark and Uk with their efficient sampling strategy often give back unreal growth advantages in the first period of spreading.
While in other countries 100 seqs could be a legitimate threshold to judge advantage or disadvantage there more time and sequences are needed (saying that after being fooled multiple times)
Still this one seems interesting it keeps some advantage also versus global dominant BA.5.2* lineage. So it is worth monitoring

[FedeGueli]

I rechecked growth advantage versus new global dominant lineage BA.5.2* :
https://cov-spectrum.org/explore/Denmark/AllSamples/Past2M/variants?variantQuery=nextcladePangoLineage%3ABA.5.2*&variantQuery1=nextcladePangoLineage%3ABA.5.1+%26+ORF1a%3AI2368T+%26+ORF1a%3AQ3922R&analysisMode=CompareToBaseline&

Advantage is slight probably non existent ,
and it turns certainly to disadvantage versus the biggest BA.5.2* sublineage with Orf1b:1050N
https://cov-spectrum.org/explore/Denmark/AllSamples/Past2M/variants?variantQuery=nextcladePangoLineage%3ABA.5.2*+%26+Orf1b%3A1050N&variantQuery1=nextcladePangoLineage%3ABA.5.1+%26+ORF1a%3AI2368T+%26+ORF1a%3AQ3922R&analysisMode=CompareToBaseline&

My view that this , interesting as it has a double mutation in orf1ab but not sufficient to overtake big & fast ba.5.2 sublineages. (and we should keep in my mind that a big lineage with 10k sequences is always LOCALLY the real competitor for any new lineage, more than a super fast little lineage that is spreading on other side of the world)

[aq-sun]

Nice one @alurqu, as ORF1a:Q3922R coincides with a geographical introduction into Denmark and therefore marks an epidemiological event, we used A12030G (ORF1a:Q3922R) as the defining mutation to designate this as BA.5.1.11, with 327 new designations and 47 updated from BA.5.1.