med-Rxiv: Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

[sharon sanders]

Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

Scott Wesley Long, Randall J Olsen, Paul A. Christensen, David W Bernard, James J. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Hung-Che Kuo, Heather Hendrickson, Ghazaleh Eskandari, Hoang A.T. Nguyen, James Hunter Long, Muthiah Kumaraswami, Jule Goike, Dani el Boutz, Jimmy Gollihar, Jason S. McLellan, Chia-Wei Chou, Kamyab Javanmardi, Ilya J. Finkelstein, James Musser

doi: https://doi.org/10.1101/2020.09.22.20199125

This article is a preprint and has not been certified by peer review [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

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Abstract


We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.

https://www.medrxiv.org/content/10.1....22.20199125v1

 

[sharon sanders]

snip

By the second wave of the outbreak in Houston, the study found that this variant had leaped to 99.9% prevalence - completing its domination of the outbreak. The researchers found that people infected with the strain had higher loads of virus in their upper respiratory tracts, a potential factor in making the strain spread more effectively.

Kristian Andersen, an immunologist at the Scripps Research Institute in California, who was not involved in the new research, downplayed the significance of the new study. He said it “just confirms what has already been described - G increased in frequency over time.” As for the numerous other mutations the study finds, “they just catalogue them, but we don’t know if any of them have any functional relevance.”

Musser said D614G has been increasingly dominant in Houston and other areas because it is better adapted to spreading among humans. He acknowledged that the scientific case is not closed on this matter.


https://www.adn.com/nation-world/20...nd-potentially-evolving-amid-rapid-us-spread/