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Compositional diversity and evolutionary pattern of coronavirus accessory proteins.

Jingzhe Shang1, Na Han1, Ziyi Chen1

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This study introduces CoroAnnoter, a tool for analyzing coronavirus accessory proteins. It reveals significant diversity in these proteins across different coronaviruses, impacting host adaptation and viral evolution.

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Area of Science:

  • Virology
  • Genomics
  • Evolutionary Biology

Background:

  • Accessory proteins are crucial for coronavirus-host interactions, influencing host adaptation and epidemic spread.
  • Understanding their diversity and evolution is key to comprehending coronavirus behavior.

Purpose of the Study:

  • To develop a standardized tool for annotating coronavirus genomes and profiling accessory proteins.
  • To analyze the composition, genomic distribution, and evolutionary patterns of coronavirus accessory proteins.
  • To compare the host interaction networks of accessory proteins from SARS-CoV-2 and SARS-CoV.

Main Methods:

  • Development of CoroAnnoter, integrating ORF prediction, transcription regulatory sequence recognition, and homologous alignment.
  • Annotation of 39 representative coronavirus strains using CoroAnnoter.
  • Comparative analysis of accessory protein composition, genomic distribution, and evolutionary trends.
  • Examination of virus-host interaction networks for SARS-CoV-2 and SARS-CoV accessory proteins.

Main Results:

  • CoroAnnoter successfully annotated coronavirus genomes, revealing significant variation (1-10 proteins) in accessory protein numbers, with SARS-CoV-2 and SARS-CoV having the most.
  • Accessory protein genomic distribution showed intra-genus conservation and inter-genus diversity, with distinct patterns for different coronavirus genera.
  • Evolutionary analysis indicated conserved accessory proteins upstream of E-M genes and diverse ones downstream.
  • Shared antiviral signaling pathways, apoptotic processes, and stress responses were identified between SARS-CoV-2 and SARS-CoV accessory protein interactions.

Conclusions:

  • The study provides a valuable tool, CoroAnnoter, for coronavirus genome annotation.
  • A comprehensive profile of coronavirus accessory proteins has been established, detailing their composition, classification, evolution, and host interactions.
  • Findings enhance understanding of coronavirus adaptation and epidemic variation, with implications for public health.