Genotyping of PCV3 based on reassembled viral gene sequences
| Autor: | Hee-Chun Chung, Yong Ho Park, Bong-Kyun Park, Van Giap Nguyen |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Circovirus
Genes Viral Genotype genetic analysis Biology Polymerase Chain Reaction Genetic analysis Viral Proteins South Korea Circoviridae Infections Clade Genotyping Gene Phylogeny Genetics lcsh:Veterinary medicine General Veterinary likelihood mapping Nucleic acid sequence Original Articles biology.organism_classification Porcine circovirus Capsid lcsh:SF600-1100 Original Article porcine circovirus type 3 |
| Zdroj: | Veterinary Medicine and Science Veterinary Medicine and Science, Vol 7, Iss 2, Pp 474-482 (2021) |
| ISSN: | 2053-1095 |
| DOI: | 10.1002/vms3.374 |
| Popis: | Porcine circovirus type 3 (PCV3) has been reported in many countries such as USA, China, Korea and many European countries during 2015–2018. The six PCV3 strains named IH, SJ, N5, N10, N13 and N62 were detected out of 220 samples by PCR methods while the prevalence our study was conducted in 2017 to 2018. The six detected strains were hard to genotype with reference viruses due to their diverse phylogenetic relationship. PCV3 capsid, ORF3 and replicase protein coding genes were reassembled at the nucleotide sequence level, then 16 new reassembled PCV3 sequences were generated. Based on the maximum likelihood mapping analysis of 303 PCV3 sequences a model with a combination of replicase, ORF3 and capsid protein coding genes was selected as the most appropriate target for genotyping, which provided the best support for the clade classification into three genotypes and several subtypes (genotype 1, genotype 2; subtype: a and b, genotype 3; subtype a, b, c, d, e, f, g, h). This study, the IH_Korea_2017 and N62_Korea_2018 strains belong to genogroup 3 (subtype a) the SJ_Korea_2017 strain genogroup 3 (subtype g) and the N5, N10, N13 Korea_ 2018 strains genogroup 3 (subtype f), respectively. In conclusion, this study may provide insights to classification of PCV3 genotypes around the world. |
| Databáze: | OpenAIRE |
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