The Omicron Anthology Series Archives
A Collection of the Preliminary Omicron Studies
This post was transferred over from Modern Discontent. If you are interested in Anthology Series posts as they come in or are interested in smaller posts along the way please consider subscribing over there as that is the main Substack. Also, paid-only content will only be available through becoming a paid member on Modern Discontent.
Far too often my posts wind up being far longer than I anticipate. When I began writing about Omicron I didn’t expect it to get that long. However, it’s become one of my longest series. Even excluding my series on monoclonal antibodies, this series alone went over 40 pages!
Here, I’ll collect them all into a “more” sharable format for those who would like to share this information, starting first with the monoclonal antibody series as these studies examined whether monoclonal antibodies work against Omicron. Then, I dive into the available studies and examine some strange behaviors of Omicron and examine if evidence of a possible animal origin for Omicron.
The Monoclonal/Omicron Anthology Series
This series was based on the first reports that monoclonal antibodies aren’t effective against Omicron. Here, I examine several studies and see if there is any veracity to the argument, covering some of the nuances of these studies.
The Curious Emergence of Omicron
Part I: Introduction and Examining Phylogenetic Trees
This series first starts off looking at what SARS-COV2 lineage may have led to Omicron. Here, an examination of phylogenetic trees suggests a possible Alpha variant to be Omicron’s ancestor.
Part II: Omicron's Vastly Different Viral Behaviors
Omicron behaves very differently from past variants. In particular, it doesn’t seem to bind to human ACEII receptors with the same affinity seen in other strains of the virus. It also does not seem to be readily cleaved by serine proteases to the same extent as well. Instead, the virus seems to spread predominately through cell-to-cell viral transmission instead.
*Additional Post Highlight from Nutrition Matters*
Several other Substacks have covered Omicron’s attenuated virulence and have provided more detail on certain aspects.
Here’s one post from the Substack by Robin Whittle, in which Robin highlights a few studies as evidence of Omicron’s attenuated nature.
One thing that Robin was able to capture that I did not find was a study in which researchers point to the endosomal pathway as a likely avenue to Omicron’s viral transmission, particularly among nasal epithelial.
The study in question is here:
https://www.biorxiv.org/content/10.1101/2021.12.31.474653v1.full
The post also provides a much better explanation for syncytia formation compared to my measly mention of the phenomenon. I highly encourage people to read this post and check out Robin’s Substack! And if anyone has any other Substack recommendations please let me know!
Part III: Loss of Neutralizing Antibodies
Paralleling what we saw with monoclonal antibodies, it seems that prior immunity to SARS-COV2 may be attenuated against Omicron. However, those who have had a booster or have had heterologous exposure to the spike antigen (through both infection and vaccination) seem to still produce neutralizing antibodies. Also, a study on T-Cell preservation explains why it’s more than just the antibodies that should matter.
Part IV: Attenuated Lung Infection, Change in Disease Pathology?
This post looks specifically at the change in Omicron’s “cells of choice”. Unlike prior strains, Omicron doesn’t seem to target the lungs to the same extent as previous strains. Paired with the evidence of Omicron’s reduced virulence, this change is likely to explain why Omicron presents with less severe symptoms. Once again, another recommendation to read the post from Nutrition Matters to add more to the discussion.
Part V-1: Mice as the Possible Origins of Omicron
This was intended to be a 2-parter, although I was able to contain most of the information into this one post (apologies for the extremely long post!). This post takes a look at the widely circulating Wei et. al. paper and breaks down the information and adding context from some of the prior studies that we examined.
Part VI: Study Limitations, Concluding Remarks, & Citations
To close out this series, I provide some criticisms for the studies that I included in this series. I also provide some criticisms with respect to the mouse origin study and add some prospective studies that could be conducted to validate this hypothesis. Finally, I provide my final thoughts and provide references.