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Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization
Published on: December 23, 2020
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Variable routes to genomic and host adaptation among coronaviruses
Vincent Montoya1, Angela McLaughlin1,2, Gideon J Mordecai3
1British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
Journal of Evolutionary Biology
|March 22, 2021
Summary
Viral adaptation via natural selection drives host colonization. Coronaviruses show diversifying selection, especially in spike genes, indicating ongoing adaptation to new hosts like humans, crucial for pandemic preparedness.
Area of Science:
- Genomics
- Evolutionary Biology
- Virology
Background:
- Natural selection on viral genomes aids adaptation and host colonization.
- Coronaviruses are a significant family of zoonotic viruses with implications for public health.
Purpose of the Study:
- To analyze and compare viral adaptation across seven Coronaviridae zoonotic events.
- To quantify rates of nonsynonymous (dN) and synonymous (dS) changes in viral genomic sequences.
- To understand the role of selection in coronavirus host shifts.
Main Methods:
- Analysis of genomic sequence data from seven zoonotic coronavirus events.
- Quantification of dN/dS ratios at specific amino acid positions for each open reading frame (ORF).
- Comparative analysis of selection pressures across primary, intermediate, and human hosts.
Main Results:
- Purifying selection dominated (77% of sites), while diversifying selection was frequent in primary hosts and the orf1ab region.
- Spike gene showed diversifying selection in intermediate hosts, linked to host entry and immune evasion.
- SARS-CoV-2 exhibits higher positive selection near glycosylation sites and suggests it's in an adaptive phase post-host switch.
Conclusions:
- Genomic adaptation, particularly in spike genes, is key to coronavirus host shifts and zoonotic potential.
- Understanding coronavirus adaptation mechanisms is vital for predicting pandemics and developing effective countermeasures.
- SARS-CoV-2's ongoing adaptation highlights the need for continued surveillance and research.
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