Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype.,Virus Evolution

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Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype.
Virus Evolution ( IF 5.3 ) Pub Date : 2023-08-18 , DOI: 10.1093/ve/vead051
Wan-Ting He _{1,

2} , Dongyan Li ₁ , Guy Baele ₂ , Jin Zhao ₁ , Zhiwen Jiang ₁ , Xiang Ji ₃ , Michael Veit ₄ , Marc A Suchard ₅ , Edward C Holmes ₆ , Philippe Lemey ₂ , Maciej F Boni , Shuo Su _{1,

7}

Affiliation

Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium.
Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA.
Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin 14163, Germany.
Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms typically associated with classical PHEV infection. Through large-scale epidemiological surveillance, we show that these novel lineages have circulated in at least eight provinces in southeastern China. Phylogenetic and recombination analyses of twenty-four genomes identified two major viral lineages causing respiratory symptoms with extensive recombination within them, between them, and between classical PHEV and the novel respiratory variant PHEV (rvPHEV) lineages. Divergence times among the sampled lineages in the PHEV virus complex date back to 1886-1958 (mean estimate 1928), with the two major rvPHEV lineages separating approximately 20 years later. Many rvPHEV viruses show amino acid substitutions at the carbohydrate-binding site of hemagglutinin esterase (HE) and/or have lost the cysteine required for HE dimerization. This resembles the early adaptation of human CoVs, where HE lost its hemagglutination ability to adapt to growth in the human respiratory tract. Our study represents the first report of the evolutionary history of rvPHEV circulating in swine and highlights the importance of characterizing CoV diversity and recombination in swine to identify pathogens with outbreak potential that could threaten swine farming.

更新日期：2023-08-18

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