Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan

Fu-Chun Hsueh; Cheng-Nan Wu; Marco Yung-Cheng Lin; Feng-Yang Hsu; Chuen-Fu Lin; Hui-Wen Chang; Jih-Hui Lin; Hsin-Fu Liu; Ming-Tang Chiou; Kuan Rong Chan; Chao-Nan Lin

doi:10.1093/ve/veab096

Phylodynamic analysis and spike protein mutations in porcine deltacoronavirus with a new variant introduction in Taiwan

Virus Evol. 2021 Nov 24;7(2):veab096. doi: 10.1093/ve/veab096. eCollection 2021.

Authors

Affiliations

¹ Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Scienceand Technology, Pingtung 912301, Taiwan.
² Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung 406053, Taiwan.
³ Department of Medical Research, Mackay Memorial Hospital, Taipei 10449, Taiwan.
⁴ Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan.
⁵ Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei 11561, Taiwan.
⁶ Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.

Abstract

Porcine deltacoronavirus (PDCoV) is a highly transmissible intestinal pathogen that causes mild to severe clinical symptoms, such as anorexia, vomiting, and watery diarrhea in pigs. By comparing the genetic sequences of the spike glycoprotein between historical and current Taiwanese PDCoV strains, we identified a novel PDCoV variant that displaced the PDCoV responsible for the 2015 epidemic. This PDCoV variant belongs to a young population within the US lineage, and infected pigs carry high concentrations of the virus. It also has several critical point mutations and an amino acid insertion at position 52 that may enhance the affinity between the B-cell epitopes located in the N-terminal domain with its complementarity regions, consequently facilitating binding or penetration between the fusion peptide and cellular membrane. Furthermore, viral protein structure prediction demonstrated that these amino acid changes may change the ability of the virus to bind to the receptor, which may consequently alter virus infectivity. Our results hence suggest the emergence of new PDCoV strains in Taiwan with the potential for greater transmission and pathogenesis.

Keywords: evolutionary rates; phylodynamics; phylogenetics; porcine deltacoronavirus; structural analysis.