- A new preprint is being used to claim “persistent immune damage” after COVID. I’ve written a detailed scientific review explaining why that conclusion does NOT follow. Small cohort. Descriptive data. Big claims. This matters open.substack.com/pu... 1/4
- This reply was hidden by the thread author.This isn't a new preprint; it came out about 4 months ago, when I wrote a 🧵 on it. Not sure why there's a sudden resurgence in interest. I find it extremely interesting because the findings are consistent with a pattern I've discovered in chronic deep-lung infections. bsky.app/profile/ryan...
- It's also consistent w/the findings of a non-human primate experiment in which macaques completely cleared all viral RNA from from their nasal tract & trachea within 3 weeks—like the typical human—but who nonetheless had elevated inflammatory markers for >1 yr (duration of study). It turned out...
- ...they had chronic infection in the alveolar compartment. A majority of macaques tested + for viral RNA (68%) or antigen (80%). The typical explanation for this is that these are fragments of lingering viral material and that no viable virus remains. But...
- They found that RNA- and antigen-positive BAL samples contained infectious virus that productively replicated in alveolar macrophages in cell culture. Even a few of the RNA- and antigen-negative samples showed evidence of productive replication (84% showed increasing levels of spike over time).
- There are many other really interesting findings in that paper—including an intriguing counterbalancing act of IFN-γ & MHC-E in alveolar macs that could help explain persistence (IFN-γ associated w/viral control but also increased MHC-E expression, which inhibits NK cytotoxicity).Jan 18, 2026 15:33
- The near absence of RBD spike muts in chronic-infection BAL-sample sequences fits neatly w/the cell-cell spread they found in alveolar macs—as do some other aspects. Less clear why this might incr E antibodies, but the extraordinarily high rate of E mutations in BAL seqs hints at a connection.
- Here's a link to that paper. There are several others that support productive infection of alveolar macrophages, though they focus on acute infection. I'd do a longer, more comprehensive thread including info from those, but I'm too exhausted & can't think right now. www.nature.com/articles/s41...
