I'd like to detail exactly why I think Dr. Gottlieb's prediction is off, but not entirely wrong, and what strains I think may be faced this winter.  His premise that Delta spreads so rapidly that it will eventually burn itself out, perhaps even before winter, is very plausible and even likely.  Note that summers will favor strains with better transmissibility, while winter will favor strains with better immune evasion, due to inoculum levels varying with temperature.

It's the idea that cross-reactivity to anti-Delta antibodies will confer broad resistance to other strains, and thus the end of the pandemic, that I disagree with.


Depending on how fast Delta mutates relative to how fast it spreads, it may not even be a progenitor of the next major strain.  I would say the odds depend on recombination and the localization of existing mutations.  If its increased transmissibility is due mostly to its increased viral load in the nasal passages, it is likely tied to proteins other than S(see N and nsp6 in particular, discussed in this paper).  A putative recombination event with a strain with a different S gene would greatly increase the chance of Delta being the basis for the next major strain.

This paper supports the idea that recombination is the major driving force in the evolution of SARS-CoV-2.  However, many case studies have also demonstrated extremely rapid intra-host evolution in protracted infections, particularly in immunocompromised individuals.  This is obliquely mentioned in the paper, but they suggest that it would have had to occur on multiple continents, thinking it thus unlikely.  I don't think it's so far-fetched: it's happened in multiple individuals in single countries.  Recombination would have had to have happened multiple times in a short time frame and few of the accumulated mutations would be novel.


I like their MJN approach, and it does tilt the scales towards recombination in widely distributed strains, though each could remedy a hard polytomy.

image.png


Regardless, the S genes from other candidate strains following a different haplotype, not likely to be strongly cross-reactive with Delta, with a phenotype more marked by immune evasion may be more likely winter wave candidates than Delta.  The highly efficacious syncytia of Delta result largely from P681R, so a candidate strain might be identified by S:E484K, N501Y, and P681H, and that includes B.1.621.  B.1.621 also has R346K for added evasion.


The failure of A.30 is peculiar to me, and may be due to missing D614G, as the rest of the virus looks quite serious.


Anyway, strains with the above haplotype have been doing quite well for themselves; their success has been concealed by the enormous spike in Delta prevalence.  Presuming that Delta burns itself out as Gottlieb suggests, they may abruptly become dominant on their own, or their S genes may be carried forward in a Delta shell through recombination.

Such recombination would create an additional wave and a worse scenario, creating a rapidly spreading strain that is also immunoevasive that should burn itself out again, but not before taking a lot of hosts out with it.  This is discussed in detail in "Recombination is the likely source for the rapidly expanding variants".
 
Whether that happens or not, we would be left with some other antigenically distant strain to take the reins, or more probably a resurgence of an antigenically drifted Delta with its own S gene as anti-Delta antibodies fade.

Comments

Popular posts from this blog

Dangerous Original Antigenic Sin Anticipated in SARS-CoV-2

Do Vaccines Prevent COVID-19, or just Delay It?