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Porcine hemagglutinating encephalomyelitis virus (PHEV), a member of the betacoronavirus genus, is widespread in swine herds and the only known coronavirus causing neurological diseases in pigs. Objective To characterize the genomic features and phylogenetic relationship of a PHEV strain isolated from China. By investigating the biological properties of the virus, we assessed its epidemiological status and identified genetic variation patterns and evolutionary trends, providing a scientific basis for developing targeted prevention and control strategies. Methods RT-PCR detection was performed on suspected PHEV-positive samples collected from a large pig farm in Jiangsu Province, China, followed by virus isolation. The isolated virus was validated by indirect immunofluorescence assay (IFA), transmission electron microscopy (TEM), and whole genome sequencing. Phylogenetic analysis was performed based on the complete genome, S gene, HE gene, and NS2 gene. Results A PHEV strain, designated as PHEV JS-2025, was successfully isolated from the brain tissue sample. IFA showed strong red fluorescence signals in the cytoplasm, and TEM revealed typical coronavirus particles with a diameter of approximate 150 nm. The strain showed vigorous propagation in HRT-18 cells, reaching the peak viral titer at 72 h, with a 50% tissue culture infectious dose (TCID50) of about 104.3 TCID50/mL. PHEV JS-2025 could infect HRT-18, NPTR, and LLC-PK1 cells, and to a lesser extent, human intestinal Caco-2 cells. Whole genome sequencing revealed that the genome of PHEV JS-2025 was 30 044 bp in length, with over 94.9% nucleotide sequence identity to 14 reference PHEV strains, clustering within the rvPHEV-L-1 lineage. Of note, a mutation in the NS2 gene caused a premature termination at amino acid 19, resulting in the functional loss of the NS2 protein. Conclusion A novel PHEV strain JS-2025 from Jiangsu Province was successfully isolated and identified. This strain exhibits unique cellular tropism and can infect human intestinal cell lines, showing a risk of cross-species transmission. The truncated NS2 gene may affect the pathogenic mechanism of this strain. This study aids in understanding the genetic evolutionary characteristics and epidemiological features of PHEV and has implications for the prevention and control of PHE.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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