Ryan Hisner

Two PJ.2.1/RC.5 recombinants were uploaded from NYC yesterday—breakpoint in the spike RBM, between S:456-S:477. Likely originated in Ontario, where RC.5 + S:I478T + S:S943G is mostly found (as @siamosolocani.bsky.social pointed out) & is therefore circulating. RC.5 is a NB.1.8.1 descendant.

PJ.2.1 is a fast-growing saltation variant descended from KP.3.1.1-->MC.10.1.7, which last circulated in early 2025 before reappearing this year, almost certainly after extensive intrahost evolution in a chronically infected patient.

66 airport SARS-CoV-2 sequences from incoming travelers were uploaded today, collected Sept 21-30, and 26 (39.4%) were PJ.2.1. 20/30 (66.7%) sequences from Latin American travelers were PJ.2.1. Seems likely that PJ.2.1 is rapidly sweeping across the entire Western hemisphere.

6/24 (25%) travel sequences from Europe were PJ.2.1: Two from the UK and one each from Belgium, Italy, Spain, and Turkey. There were no PJ.2.1 sequences from Africa (0/4) or Asia (0/8). Very few mutations in these sequences, likely a sign of rapid PJ.2.1 growth.

3/33 sequences from New Zealand uploaded today are PJ.2.1. All three very recently collected though, so that 3/11 of the most recent sequences (since Sept 26) are PJ.2.1, meaning it could already be significantly higher than 10% prevalence. PJ.2.1 growth seems to be accelerating of late.

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

And as long as that's the case—and I think it will be the case as long as the evidence, however convincing, remains indirect—there's basically no chance there will be concerted public health efforts to identify and treat chronic infections.

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

Second, it seems this person is continuing to shed diverse variants, some of which have the potential to spread and possibly cause an increase in Covid cases worldwide. Not an ideal situation for society, so there's a global public health interest here, in my opinion.

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

First, there's almost certainly at least 1 person suffering a chronic infection without knowing it—sequences are never shared w/patients, AFAIK, which I consider unethical, but which seems to be standard practice. (I called the company that did my + PCR test asking for info & was stonewalled.)

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

While I think the most likely explanation is that each of these diverse PJ* variants evolved in & were/are being transmitted from the same person, it's also possible that a small # of closely connected, relatively isolated individuals w/chronic infections are the source.

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

And obviously, these did not evolve stepwise during circulation, which would require dozens & dozens of repeated reversions & repeated evolution of identical mutations, deletions, & insertions. To me, there's only one plausible explanation for this: intrahost evolution. bsky.app/profile/ryan...

Large upload from Ontario yesterday, providing some striking revelations about the evolution of PJ.2.1. First, there is yet another strikingly divergent branch of PJ.2.1. This isn't one variant: it's four. More and more, this resembles the emergence of BA.1/2/3. What is happening? 1/

I wonder if this is due to Japan's more successful avoidance of pre-Omicron infection—emphasizing ventilation, masking, & avoiding crowded indoor spaces, which undoubtedly saved countless lives—making their infection history more similar to that of young children (which BA.3.2 is known to prey on).

3rd independent branch of PJ.2.1 with S:A475V appeared today. This seems to be a winning mutation in PJ.2.1, which has excess ACE2 affinity to burn. However, all 3 branches are singlets so far, so it hasn't caught fire or anything. PJ.2.1 at 25% in Maryland in very recent samples, as Fede says 👇