Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E

  1. Kathryn E Kistler  Is a corresponding author
  2. Trevor Bedford
  1. University of Washington, United States
  2. Fred Hutchinson Cancer Research Center, United States

Abstract

Seasonal coronaviruses (OC43, 229E, NL63 and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here, we address the influence of antigenic drift on immune evasion of seasonal coronaviruses. We provide evidence that at least two of these viruses, OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein that are exposed to human humoral immunity. This suggests that reinfection may be due, in part, to positively-selected genetic changes in these viruses that enable them to escape recognition by the immune system. It is possible that, as with seasonal influenza, these adaptive changes in antigenic regions of the virus would necessitate continual reformulation of a vaccine made against them.

Data availability

All data used in this study can be found at https://www.viprbrc.org/ or in the Github repository for this project: https://github.com/blab/seasonal-cov-adaptive-evolution.

Article and author information

Author details

  1. Kathryn E Kistler

    Molecular and Cellular Biology, University of Washington, Seattle, United States
    For correspondence
    kistlerk@uw.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3216-0020
  2. Trevor Bedford

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4039-5794

Funding

National Science Foundation (Graduation Research Fellowship Program,DGE-1762114)

  • Kathryn E Kistler

Pew Charitable Trusts (Pew Biomedical Scholar,NIH R35 GM119774-01)

  • Trevor Bedford

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Kistler & Bedford

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 9,873
    views
  • 1,254
    downloads
  • 88
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Kathryn E Kistler
  2. Trevor Bedford
(2021)
Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E
eLife 10:e64509.
https://doi.org/10.7554/eLife.64509

Share this article

https://doi.org/10.7554/eLife.64509

Further reading

    1. Evolutionary Biology
    Nagatoshi Machii, Ryo Hatashima ... Masato Nikaido
    Research Article

    Cichlid fishes inhabiting the East African Great Lakes, Victoria, Malawi, and Tanganyika, are textbook examples of parallel evolution, as they have acquired similar traits independently in each of the three lakes during the process of adaptive radiation. In particular, ‘hypertrophied lip’ has been highlighted as a prominent example of parallel evolution. However, the underlying molecular mechanisms remain poorly understood. In this study, we conducted an integrated comparative analysis between the hypertrophied and normal lips of cichlids across three lakes based on histology, proteomics, and transcriptomics. Histological and proteomic analyses revealed that the hypertrophied lips were characterized by enlargement of the proteoglycan-rich layer, in which versican and periostin proteins were abundant. Transcriptome analysis revealed that the expression of extracellular matrix-related genes, including collagens, glycoproteins, and proteoglycans, was higher in hypertrophied lips, regardless of their phylogenetic relationships. In addition, the genes in Wnt signaling pathway, which is involved in promoting proteoglycan expression, was highly expressed in both the juvenile and adult stages of hypertrophied lips. Our comprehensive analyses showed that hypertrophied lips of the three different phylogenetic origins can be explained by similar proteomic and transcriptomic profiles, which may provide important clues into the molecular mechanisms underlying phenotypic parallelisms in East African cichlids.