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Adaptive Evolution of the Spike Protein in Coronaviruses

Xiaolu Tang1, Zhaohui Qian2, Xuemei Lu3,4

  • 1State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.

Molecular Biology and Evolution
|April 13, 2023
PubMed

Insights

The Spike (S) gene in coronaviruses, including SARS-CoV-2, shows positive selection. This evolution, especially in the S1 receptor-binding domain, is driven by host shifts and human interventions like vaccination.

Area of Science:

  • Virology
  • Molecular Evolution
  • Genomics

Background:

  • Coronaviruses are RNA viruses infecting mammals and birds.
  • The Spike (S) protein mediates host cell entry via receptor binding.
  • S protein evolution is complex, with varying receptor interactions across genera.

Purpose of the Study:

  • To investigate selection pressures on the coronavirus Spike (S) gene.
  • To compare evolutionary patterns between SARS-CoV-2 and other coronaviruses.
  • To understand the impact of host shifts on S gene evolution.

Main Methods:

  • Phylogenetic analysis of coronavirus S genes.
  • Identification of positively selected sites within the S gene.
  • Comparative analysis across different coronavirus genera.

Main Results:

  • The S gene, particularly the S1 region, is under positive selection in both SARS-CoV-2 and other coronaviruses.
  • Positive selection signals are observed in the S1 N-terminal domain across all four genera.
  • Ongoing SARS-CoV-2 evolution shows primary positive selection in the S1 C-terminal (receptor-binding) domain.

Conclusions:

  • The S gene experiences significant positive selection, crucial for viral adaptation.
  • SARS-CoV-2's evolution highlights selection pressure on the receptor-binding domain, influenced by human adaptation and interventions.
  • Understanding these evolutionary dynamics is key to managing coronavirus outbreaks.
Keywords:
SARS-CoV-2Spike proteinadaptive evolutioncoronavirusmolecular evolutionpositive selection

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