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Update recombinant descriptions
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corneliusroemer committed Mar 5, 2024
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7 changes: 4 additions & 3 deletions reports/variant_report_latest_draft.md
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Expand Up @@ -23,11 +23,12 @@ Below is a summary of notable lineages with at least 2 of the 3 mutations:

Around 3-4% of sequences collected globally at the beginning of February are from recombinants that have JN.1 spike with some other part of the genome derived from an XBB donor.

As spike is the major determinant of the virus's antigenic properties and fitness, these recombinants are not fundamentally different from JN.1\* lineages. Nonetheless, it is worth monitoring them, not the least because their names do not readily reveal their JN.1 spike origin:
As spike is the major determinant of the virus's antigenic properties and fitness, these recombinants are not fundamentally different from JN.1\* lineages. Nonetheless, it is worth monitoring them, not the least because their names do not readily reveal their BA.2.86 spike origin:

- XDD: 3-5% in Italy/Spain, no sign of growth advantage over JN.1
- XDD: Common across world but no sign of growth advantage over JN.1
- XDK: S:T572I inherited from JN.1.1.1, but without JN.1.1's deleterious ORF1a:F499L, most common in France at around 10-15% beginning of February 2024, followed by Greece and New Zealand where it is around 5%. No sign it is any different than the JN.1\* lineage with S:T572I.
- XDP: JN.1.1 with 3' end from FL.15.1.1 (XBB\*), therefore with ORF8:G8\*, ORF9b:I5T. 1% in USA in February 2024, relative growth advantage of around 20%/week vs JN.1 (30% vs JN.1.1, as JN.1.1 has disadvantage vs JN.1).
- XDP: JN.1.4 with 3' end from FL.15 (XBB\*), therefore with ORF8:G8\*, ORF9b:I5T. 1% in USA in February 2024, relative growth advantage of around 20%/week vs JN.1 (30% vs JN.1.1, as JN.1.1 has disadvantage vs JN.1).
- XDQ: BA.2.86.1 with 3' from FL.15.1.1, lacks S:L455S as not from JN.1 but sublineage XDQ.1 has S:A475V. Around 5% at end of January 2024 in South Korea and Japan, possibly growing.
- XDR: ORF1a from JD.1.1.1, rest from JN.1.1. Most common in Brazil at up to 20% at the beginning of February 2024, relative growth advantage unclear, likely not very big as no strong growth outside Brazil.
- XDS differs from the other recombinants in that it has its spike from JN.3.2.1 (which has S:F456V instead of S:L455S). It also has 3' from XBB with ORF8:G8\*, ORF9b:I5T. Around 1% in the UK.

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