Is SARS-CoV-2 running out of evolutionary space? Is variant evolution slowing down? Is immune escape unlikely anymore? Let's explore. 🧵
Here are some phylogenies (evolutionary trees) of the major SARS-CoV-2 variant lineages from . One is in radial format, the other unrooted, but they show the same information and are both scaled to divergence (number of mutations). nextstrain.org
And here are some plots of mutations over time, again from . There is no sign of this rate of accumulation of mutations slowing down (if anything, more recent variants are above the trend line). nextstrain.org
It's worth looking at spike (S1) mutations specifically. Note two things here:
1) We're still getting a LOT of new mutations.
2) These come in rather discrete jumps, then a flatter plateau. That's because of recombination or within-host evolution in persistent infections.
Here is some info on immune escape and ACE2 binding -- that is, how well the variant avoids existing antibodies and how well it can attach to the receptors on our cells. The top right is the "uh oh" zone where it is good at both. From . nextstrain.org
Looking at global trends for immune escape and ACE2 binding for the last 20 days, we see lots of variants with very high immune escape compared to BA.2, and some that also have high ACE2 binding. Note the change between BA.2.86 (circled) and its descendants. From @RajlabN.
Here's immune escape (vs. BA.2) over time, from . Again, the virus is not running out of ways to escape current immunity (which is partial, temporary, and changing according to vaccinations and infections). From . nextstrain.org nextstrain.org
Why does this keep happening, contrary to minimizer assumptions? Because:
1) Orgel's second rule: "Evolution is cleverer than you are".
2) This:
A reminder about Greek letters and the decision to keep calling everything "Omicron".
When you're accustomed to extreme privilege, feeling uncomfortable becomes feeling unsafe, and those feelings become more important than other people's lives.
And that's the most generous explanation for why one of these bothers some folks way more than the other. There are far more disturbing explanations, of course.
“I have almost reached the regrettable conclusion that the Negro’s great stumbling block in the stride toward freedom is not the White Citizens Councilor or the Ku Klux Klanner but the White moderate who is more devoted to ‘order’ than to justice.” - MLK
The best we get now is *relative* lows. Here are numbers of hospital patients with COVID in Canada. It's as low as it has been since the first Omicron wave (early 2022), on par with the relative lull of mid-summer 2023. But still much higher than summer 2020 and summer 2021.
*Maybe* it will continue to drop as thr weather warms and if there are no new major variants that displace JN.1* in the meantime (fingers crossed, and wastewater signal is low), but the reality is that the baseline has never come back down in Canada post-Omicron.
Relative lows do not mean no risk, they mean less risk. If you've been putting off doing things while cases were higher, a relative low is a better (but again, not risk-free) time to do them than during a relative high, obviously.
1. Israeli real estate companies held Jews-only events to sell land in Israel and contested (Jerusalem) or occupied (West Bank) territories in Palestine.
Note that some of the events are taking place in synagogues and some include properties that are within the illegally occupied West Bank. Other events have been held at public venues.
Now that Pirola clan (BA.2.86 and descendants, most notably JN.1*) is the dominant variant lineage globally, the question arises as to whether it might undergo recombination with earlier XBB lineages.
Yep. Already has.
🧵
So far...
Pirola x Arcturus:
XDK = JN.1.1.1 x XBB.1.16.11
Pirola x Eris:
XDD = JN.1 x EG.5.1.1
XDS = JN.3.2.1 x EG.5.1.3
Pirola x Kraken:
XDN = JN.1. x JD.1*
XDR = JN.1.1 x JD.1.1.1
Here are some excellent threads about more highly divergent BA.2 lineage variants showing up after having evolved within a single host with a chronic infection. Within-host evolution is going to be an increasingly important issue.