Lots of recombinants these days, but it's rare to see one involving BA.1. But a BA.1.17/KP.3.1.1 recombinant showed up today. Clean breakpoint near the end of ORF1a.
Has ~25 private AA mutations in the BA.1.17-inherited ORF1a—many classic chronic-infection mutations—but only a few elsewhere. 1/4
Has ~25 private AA mutations in the BA.1.17-inherited ORF1a—many classic chronic-infection mutations—but only a few elsewhere. 1/4
Comments
The retention of the BA.1 ORF1a makes it clear this person has been continuously infected for over 3 years, but I have to wonder.... 2/4
• Many chronic infections cannot be detected via traditional nasal swabs as they inhabit the deep lung, GI tract, or other bodily niche
• Undersampling in regions of the world likely to have higher rates of chronic infection
• Oversampling of patients w/cancer or other condition they're being treated for
The KP.3.1.1 portion is from mid-late 2024, though it's not possible to locate the exact branch as there are several equally plausible candidates.
Within the US, states will vary a lot too. New York, e.g., would have a much higher JN.1%
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Armchair scientist here, not a pro. 3/3