Tuesday, March 16, 2021

03.15.2021 Update: Successful Mass Vaccinations or Mass Deaths?

 "The vast majority of V2 and V3 variants and some more recent V1 variants also have a spike E484K mutation. Whereas in the presence of 501N, 484K has a modest positive impact on ACE2 binding 9, when present with 501Y, these mutations together synergistically increase ACE2-RBD binding affinity ~12.7 fold ... Crucially, E484K and other mutations at S/484 also frequently confer protection from neutralization by both convalescent sera ... , vaccine elicited antibodies ... , and some monoclonal antibodies ... There is therefore increasing evidence that viruses carrying the E484K mutation (with or without 501Y) will be able to more frequently infect both previously infected ... and vaccinated individuals ..." 

"The most important issue here is not whether this particular 'super variant' ever arises, but rather that the convergent mutations that have already arisen in members of the different 501Y lineages implies that these viruses are presently on, and are actively scaling, a broad new peak in the fitness landscape. Whatever SARS-CoV-2 variants eventually summit that peak could be a considerably bigger problem for us than any variants that we currently know in that they might have any combinations of increased transmissibility, altered virulence and/or increased capacity to escape population immunity."

"The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape" 

'20I/501Y.VI' ('B.1.1.7')

'B.1.1.7' is original South England "Variant of Concern" that now accounts for .95 of the cases in England but only .07 in US. Looks like it is pretty much taking over in Whatcom County. The nomeclature is messy:  The 'B.1.1.7' variant is the clade/lineage '20I/501Y.VI'  and is also the labeled lineage/strain 'S.501Y.V1'. In addition SARS-CoV-2 '501Y lineages’ are: 

  • B.1.1.7
  • B.1.351
  • P.1

These lineages share 'convergent evolution', an important virological concept which is discussed at least here:  A compelling look at viral strains worldwide over time can be found at This site that uses GISAID data was slow to load for me.

Nextstrain/GISAID gives that clade/variant/lineage the brightest red color of all the variants:

'20I/501Y.VI' ('B.1.1.7') is clearly a dangerous and possibly highly transmissible variant.  Neither Pfizer nor Moderna may be effective as desired against this strain. See

'20I/501Y.VI' ('B.1.1.7') is a small part of WA variants to date, but it looks like we are helping lead the way in spread 20I in WA from Whatcom County. Click on the red dots:  This is the (Trevor) Bedford labs GISAID 'clone' (?) that allows for granular WA State and WA County searches :

A thread compiled from the tweets of Dr. Trevor Bedford of Fred Hutchinson may help explain what 'B.1.1.7' evolution means for the next few months:

Many New Variants but Poor Communication?

There are now many "variants" being discovered. See New variants include a new group discovered in the US recently. See

We may not be communicating well or clear enough about the nature of this disease in part because concepts like 'immunity escape', 'convergent evolution', 'sterilizing immunity' are not easily understood. I sense many have had enough of lockdowns, business closure, social isolation, and NPIs in general:. In a bouncy place for kids last Friday: very few masks, about 150 adults and children inside. Many adults talking face to face with no masks. Crossing the street last week, put on my mask. Gentlemen moving in wheelchair in crosswalk approaching yells out: "Don't worry. I am fully vaccinated". 

The public may not understand that the vaccinated can possibly still shed virus because mRNA vaccines are essentially 'treatments' against disease and not 'sterilizing immunity'. The probability of fully vaccinated adults becoming 'asymptomatic spreaders' of new variants is being actively discussed pro and con by researchers. Many new variants may 'escape the immunity' of the current vaccines. In light of this, the new CDC instructions on the new "freedoms of the vaccinated" may be contradictory and perhaps dangerous. From :

"If you’ve been fully vaccinated:

You can gather indoors with fully vaccinated people without wearing a mask.

You can gather indoors with unvaccinated people from one other household (for example, visiting with relatives who all live together) without masks, unless any of those people or anyone they live with has an increased risk for severe illness from COVID-19.

If you’ve been around someone who has COVID-19, you do not need to stay away from others or get tested unless you have symptoms."

Vaccine Skepticism and Hesitancy and the Next Wave

Germany, Greece, Italy, Portugal, Egypt are already saying their "third wave" is here. Italy has lockdowns scheduled for Easter.  Continuing mass vaccinations is considered possibly dangerous by some if new variants are spreading  while we are still vaccinating many for older strains. This argument paraphrased is: "Your new mRNA software upgrade may prevent out your own effective natural immunity when faced with new variants the  current vaccines cannot defeat." The absolute tragedy of such a possibility is now being openly discussed by this scholar: Dr. Bosche's arguments are compelling but like much of immunology, they are difficult for lay people to understand, let alone verify:

However, if arguments of  Dr. Bossche are correct, then the world will have made a tragic mistake with our mass vaccination campaign. Currently, Europe has paused the vaccination rollout based on fears about Astra Zeneca's safety:

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