Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China
Abstract Background Atypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow ab...
| Main Authors: | , , , , |
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| Format: | Article |
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BMC
2023-11-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-023-02247-0 |
| _version_ | 1827604380022472704 |
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| author | Xiaoyu Sun Qiaoya Zhang Hu Shan Zhi Cao Juan Huang |
| author_facet | Xiaoyu Sun Qiaoya Zhang Hu Shan Zhi Cao Juan Huang |
| author_sort | Xiaoyu Sun |
| collection | DOAJ |
| description | Abstract Background Atypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow abortion, or on coinfection with other viruses. In China, reported APPV strains were mainly isolated from South China and Central China, and data about the APPV genome from northern China are relatively scarce. Methods Eleven umbilical cords, one placenta, and one aborted piglet, were collected from aborted sows of the same farm in Shandong Province of northern China. Nucleic acids were extracted from the above samples, and subsequently pooled for viral metagenomics sequencing and bioinformatics analysis. The viral coexistence status and complete genome characteristics of APPV in Shandong Province were determined. Results In abortion cases, APPV was present with Getah virus, porcine picobirnavirus, porcine kobuvirus, porcine sapovirus, Po-Circo-like virus, porcine serum-associated circular virus, porcine bocavirus 1, porcine parvovirus 1, porcine parvovirus 3 and porcine circovirus 3, etc. The first complete genome sequence(11,556 nt) of APPV in Shandong Province of northern China, was obtained using viral metagenomics and designated APPV-SDHY-2022. Comparison with Chinese reference strains revealed that the polyprotein of APPV-SDHY-2022 shared 82.6-84.2%, 93.2-93.6%, and 80.7-85% nucleotide identity and 91.4-92.4%, 96.4-97.7%, and 90.6-92.2% amino acid identity with those of the Clade I, Clade II and Clade III strains, respectively. Phylogenetic analysis based on the complete polyprotein CDS and NS5A sequences concluded that APPV-SDHY-2022 belongs to Clade II. Analysis of the NS5A nucleotide sequences revealed homology of greater than 94.6% for the same isoform, 84.7-94.5% for different isoforms of the same clade and 76.8-81.1% for different clades. Therefore, Clade II was further divided into three subclades, and APPV-SDHY-2022 belonged to subclade 2.3. Members of Clade II have 20 unique amino acids in individual proteins, distinguishing them from Clade I and Clade III members. The E2 protein showed the greatest diversity of putative N-glycosylation sites with 9 patterns, and APPV-SDHY-2022 along with other Chinese APPV strains shared the conserved B-cell conformational epitope residues 39E, 70R, 173R, 190K and 191N of the E2 protein. Conclusions We reported viral coexistence and the first complete genome sequence of APPV from abortion cases and from Shandong Province. The new APPV isolate belongs to an independent branch of Clade II. Our results increase the molecular and epidemiological understanding of APPV in China. |
| first_indexed | 2024-03-09T05:58:12Z |
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| id | doaj.art-5263d9f27f214b0cad66d12a15cde621 |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-09T05:58:12Z |
| publishDate | 2023-11-01 |
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| spelling | doaj.art-5263d9f27f214b0cad66d12a15cde6212023-12-03T12:11:35ZengBMCVirology Journal1743-422X2023-11-0120111310.1186/s12985-023-02247-0Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, ChinaXiaoyu Sun0Qiaoya Zhang1Hu Shan2Zhi Cao3Juan Huang4College of Veterinary Medicine, Qingdao Agricultural UniversityCollege of Veterinary Medicine, Qingdao Agricultural UniversityCollege of Veterinary Medicine, Qingdao Agricultural UniversityCollege of Veterinary Medicine, Qingdao Agricultural UniversityCollege of Veterinary Medicine, Qingdao Agricultural UniversityAbstract Background Atypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow abortion, or on coinfection with other viruses. In China, reported APPV strains were mainly isolated from South China and Central China, and data about the APPV genome from northern China are relatively scarce. Methods Eleven umbilical cords, one placenta, and one aborted piglet, were collected from aborted sows of the same farm in Shandong Province of northern China. Nucleic acids were extracted from the above samples, and subsequently pooled for viral metagenomics sequencing and bioinformatics analysis. The viral coexistence status and complete genome characteristics of APPV in Shandong Province were determined. Results In abortion cases, APPV was present with Getah virus, porcine picobirnavirus, porcine kobuvirus, porcine sapovirus, Po-Circo-like virus, porcine serum-associated circular virus, porcine bocavirus 1, porcine parvovirus 1, porcine parvovirus 3 and porcine circovirus 3, etc. The first complete genome sequence(11,556 nt) of APPV in Shandong Province of northern China, was obtained using viral metagenomics and designated APPV-SDHY-2022. Comparison with Chinese reference strains revealed that the polyprotein of APPV-SDHY-2022 shared 82.6-84.2%, 93.2-93.6%, and 80.7-85% nucleotide identity and 91.4-92.4%, 96.4-97.7%, and 90.6-92.2% amino acid identity with those of the Clade I, Clade II and Clade III strains, respectively. Phylogenetic analysis based on the complete polyprotein CDS and NS5A sequences concluded that APPV-SDHY-2022 belongs to Clade II. Analysis of the NS5A nucleotide sequences revealed homology of greater than 94.6% for the same isoform, 84.7-94.5% for different isoforms of the same clade and 76.8-81.1% for different clades. Therefore, Clade II was further divided into three subclades, and APPV-SDHY-2022 belonged to subclade 2.3. Members of Clade II have 20 unique amino acids in individual proteins, distinguishing them from Clade I and Clade III members. The E2 protein showed the greatest diversity of putative N-glycosylation sites with 9 patterns, and APPV-SDHY-2022 along with other Chinese APPV strains shared the conserved B-cell conformational epitope residues 39E, 70R, 173R, 190K and 191N of the E2 protein. Conclusions We reported viral coexistence and the first complete genome sequence of APPV from abortion cases and from Shandong Province. The new APPV isolate belongs to an independent branch of Clade II. Our results increase the molecular and epidemiological understanding of APPV in China.https://doi.org/10.1186/s12985-023-02247-0Atypical porcine pestivirus (APPV)Viral metagenomicsAbortion casesPhylogenetic analysis |
| spellingShingle | Xiaoyu Sun Qiaoya Zhang Hu Shan Zhi Cao Juan Huang Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China Virology Journal Atypical porcine pestivirus (APPV) Viral metagenomics Abortion cases Phylogenetic analysis |
| title | Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China |
| title_full | Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China |
| title_fullStr | Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China |
| title_full_unstemmed | Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China |
| title_short | Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China |
| title_sort | genome characteristics of atypical porcine pestivirus from abortion cases in shandong province china |
| topic | Atypical porcine pestivirus (APPV) Viral metagenomics Abortion cases Phylogenetic analysis |
| url | https://doi.org/10.1186/s12985-023-02247-0 |
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