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The evolutionary dynamics of endemic human coronaviruses
Wendy K Jo1, Christian Drosten1,2, Jan Felix Drexler1,2
1Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany.
Virus Evolution
|March 26, 2021
Summary
Community immunity drives viral evolution, impacting influenza and coronaviruses. While both exhibit antigenic drift, human coronaviruses (HCoV) show slower evolution and fewer adaptive changes than influenza A virus (IAV).
Area of Science:
- Virology
- Evolutionary Biology
- Immunology
Background:
- Community immunity influences RNA virus evolution by selecting for antigenic variants.
- Antigenic drift, a key factor in influenza vaccine updates, is poorly understood in coronaviruses.
- Seasonal human coronaviruses (HCoV) and SARS-CoV-2 likely originated from animal reservoirs.
Purpose of the Study:
- To compare the long-term evolutionary dynamics of endemic human coronaviruses (HCoV-229E, HCoV-OC43) with influenza A virus (IAV) subtype H3N2.
- To investigate the extent of antigenic drift in HCoV glycoprotein genes, particularly the spike (S) protein.
- To predict potential evolutionary trajectories of SARS-CoV-2 based on endemic coronavirus and IAV evolution.
Main Methods:
- Phylogenetic analysis (Maximum Likelihood, Bayesian) of publicly available viral gene datasets spanning approximately three decades.
- Inference of evolutionary rates and selection pressures on viral glycoprotein genes (S and HA).
- Analysis of non-synonymous mutations (dN) and positively selected sites, focusing on receptor binding domains (RBD).
Main Results:
- Both HCoV and IAV exhibited tree shapes indicative of antigenic drift.
- HCoV evolutionary rates were approximately fourfold lower than IAV, with significantly fewer accumulated non-synonymous mutations.
- Receptor binding domains (RBD) showed higher rates of adaptive evolution in both HCoV and IAV, with a majority of positively selected sites located within the RBD.
Conclusions:
- Endemic HCoV undergo antigenic drift at a lower scale compared to IAV.
- SARS-CoV-2 evolution may initially resemble IAV, necessitating regular vaccine updates.
- Post-pandemic SARS-CoV-2 evolution might exhibit greater stability, similar to endemic HCoV.
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