Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018
| Autor: | Jiyong Zhou, Jing Lei, Gang Xing, Yu Zhang, Jinyan Gu, Ao Liao, Yao Cheng, Jing Yu, Liuyang Du, Xue Lian |
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| Rok vydání: | 2019 |
| Předmět: |
Gene Expression Regulation
Viral 0301 basic medicine Microbiology (medical) China Lineage (genetic) Pharmacogenomic Variants Swine Spike gene 030106 microbiology Genome Viral Biology Polymerase Chain Reaction Microbiology Article 03 medical and health sciences Monophyly Porcine epidemic diarrhoea virus Genetics medicine Animals Molecular Biology Gene Phylogeny Ecology Evolution Behavior and Systematics Swine Diseases Phylogenetic analysis Phylogenetic tree Porcine deltacoronavirus medicine.disease Virology Coronavirus Amino acid substitutions 030104 developmental biology Infectious Diseases Spike Glycoprotein Coronavirus Coinfection |
| Zdroj: | Infection, Genetics and Evolution |
| ISSN: | 1567-1348 |
| Popis: | Porcine deltacoronavirus (PDCoV) has been emerging in several swine-producing countries for years. In our study, 719 porcine diarrhoea samples from 18 provinces in China were collected for PDCoV and porcine epidemic diarrhoea virus (PEDV) detection. The epidemiological survey revealed that the positive rates of PDCoV, PEDV and coinfection were 13.07%, 36.72% and 4.73%, respectively. The entire spike (S) genes of eleven detected PDCoV strains were sequenced. Phylogenetic analysis showed that the majority of PDCoVs could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage. The China and the Viet Nam/Laos/Thailand lineages showed much greater genetic divergences than the USA/Japan/South Korea lineage. The present study detected one new monophyletic branch that contained three PDCoVs from China, and this branch was separated from the China lineage but closely related to the Viet Nam/Laos/Thailand lineage. The strain CH-HA2-2017, which belongs to this new branch, had a possible recombination event between positions 27 and 1234. Significant amino acid substitutions of PDCoV S proteins were analysed and displayed with a three-dimensional cartoon diagram. The visual spatial location of these substitutions gave a conformational-based reference for further studies on the significance of critical sites on the PDCoV S protein. Highlights • The majority of global PDCoVs could be divided into three lineages. • Three sequenced PDCoVs from China were closely related to the Viet Nam/Laos/Thailand lineage. • The China lineage showed the greatest genetic divergence. • One sequenced strain CH-HA2–2017 had a possible recombination event. |
| Databáze: | OpenAIRE |
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