Journal of Veterinary Science

The Korean Society of Veterinary Science (대한수의학회)
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Receptor binding motif surrounding sites in the Spike 1 protein of infectious bronchitis virus have high susceptibility to mutation related to selective pressure

  • Seung-Min Hong (Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University) ;
  • Seung-Ji Kim (Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University) ;
  • Se-Hee An (Animal and Plant Quarantine Agency) ;
  • Jiye Kim (Animal and Plant Quarantine Agency) ;
  • Eun-Jin Ha (Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University) ;
  • Howon Kim (Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University) ;
  • Hyuk-Joon Kwon (BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University) ;
  • Kang-Seuk Choi (Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University)
  • Received : 2023.02.03
  • Accepted : 2023.05.17
  • Published : 2023.07.31
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Abstract

Background: To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants. Objective: This study aims to investigate the putative major amino acid substitutions for the variants in GI-19. Methods: The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3). Results: Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1. Conclusions: Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.

Keywords

Acknowledgement

This work was supported by the New Faculty Startup Fund from Seoul National University (550-20200061), BK 21 plus program for Veterinary Science Research and National Institute of Wildlife Disease Control and Prevention as "Specialized Graduate School Support Project for Wildlife Disease Specialists". We also received support from Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through Animal Disease Control Technology Development Program (Development of a serious game-based global education and training system for livestock-related workers against emerging animal diseases), funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (122015-2).

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