Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars
In Korea, three genotypes of porcine circovirus type 2 (PCV2a, PCV2b, and PCV2d) have been identified on domestic pig farms, while two genotypes (PCV2a and PCV2b) have been identified in wild boar populations. Here, we investigated genotype diversity and genotypic shift in 91 PCV2 isolates from 1340...
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MDPI AG
2020-06-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/9/6/457 |
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| author | Sok Song Gyu-Nam Park SeEun Choe Ra Mi Cha Song-Yi Kim Bang-Hun Hyun Bong-Kyun Park Dong-Jun An |
| author_facet | Sok Song Gyu-Nam Park SeEun Choe Ra Mi Cha Song-Yi Kim Bang-Hun Hyun Bong-Kyun Park Dong-Jun An |
| author_sort | Sok Song |
| collection | DOAJ |
| description | In Korea, three genotypes of porcine circovirus type 2 (PCV2a, PCV2b, and PCV2d) have been identified on domestic pig farms, while two genotypes (PCV2a and PCV2b) have been identified in wild boar populations. Here, we investigated genotype diversity and genotypic shift in 91 PCV2 isolates from 1340 wild boars captured in South Korea between 2013 and 2017. Phylogenetic analyses based on the complete ORF2 showed that the 91 PCV2 strains were detected as four genotypes by qPCR screening assay: PCV2a (2.2%, 2/91), PCV2b (16.5%, 15/91), PCV2d (80.2%, 73/91), and PCV2h (1.1%, 1/91). Only one intergenotype recombinant event was detected between PCV2 ORF2 in wild boars (PCV2b) and domestic pigs (PCV2a). Amino acid positions 86–89 within ORF2, which distinguishes the different genotypes, were conserved in all PCV2 genotypes isolated from South Korean wild boars, including TNKI in PCV2a/PCV2h, SNPR in PCV2b, and SNPL in PCV2d. The estimated nucleotide substitution rates in the ORF2 region of viruses from South Korean wild boars and domestic pigs were 5.8145 × 10<sup>−4</sup> and 4.5838 × 10<sup>−4</sup> substitutions per site per year (s/s/y), respectively. The times to the most recent common ancestor (tMRCA) for South Korean domestic pig PCV2 were 1937 (PCV2a), 1972 (PCV2b), 1999 (PCV2d-1), and 2000 (PCV2d-2). By contrast, the tMRCA for South Korean wild boar PCV2b and PCV2d were 1989 and 2001, respectively. Thus, the PCV2d genotype is prevalent among South Korean wild boars and domestic pigs. |
| first_indexed | 2024-03-10T19:16:55Z |
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| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-10T19:16:55Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
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| series | Pathogens |
| spelling | doaj.art-5b44cead658848e7a36487a27ba074ca2023-11-20T03:18:25ZengMDPI AGPathogens2076-08172020-06-019645710.3390/pathogens9060457Genetic Diversity of Porcine Circovirus Isolated from Korean Wild BoarsSok Song0Gyu-Nam Park1SeEun Choe2Ra Mi Cha3Song-Yi Kim4Bang-Hun Hyun5Bong-Kyun Park6Dong-Jun An7Virus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaVirus Disease Division, Animal and Plant Quarantine Agency, Gimchen, Gyeongbuk-do 39660, KoreaIn Korea, three genotypes of porcine circovirus type 2 (PCV2a, PCV2b, and PCV2d) have been identified on domestic pig farms, while two genotypes (PCV2a and PCV2b) have been identified in wild boar populations. Here, we investigated genotype diversity and genotypic shift in 91 PCV2 isolates from 1340 wild boars captured in South Korea between 2013 and 2017. Phylogenetic analyses based on the complete ORF2 showed that the 91 PCV2 strains were detected as four genotypes by qPCR screening assay: PCV2a (2.2%, 2/91), PCV2b (16.5%, 15/91), PCV2d (80.2%, 73/91), and PCV2h (1.1%, 1/91). Only one intergenotype recombinant event was detected between PCV2 ORF2 in wild boars (PCV2b) and domestic pigs (PCV2a). Amino acid positions 86–89 within ORF2, which distinguishes the different genotypes, were conserved in all PCV2 genotypes isolated from South Korean wild boars, including TNKI in PCV2a/PCV2h, SNPR in PCV2b, and SNPL in PCV2d. The estimated nucleotide substitution rates in the ORF2 region of viruses from South Korean wild boars and domestic pigs were 5.8145 × 10<sup>−4</sup> and 4.5838 × 10<sup>−4</sup> substitutions per site per year (s/s/y), respectively. The times to the most recent common ancestor (tMRCA) for South Korean domestic pig PCV2 were 1937 (PCV2a), 1972 (PCV2b), 1999 (PCV2d-1), and 2000 (PCV2d-2). By contrast, the tMRCA for South Korean wild boar PCV2b and PCV2d were 1989 and 2001, respectively. Thus, the PCV2d genotype is prevalent among South Korean wild boars and domestic pigs.https://www.mdpi.com/2076-0817/9/6/457PCV2wild boarrecombinationtMRCAgenotype shift |
| spellingShingle | Sok Song Gyu-Nam Park SeEun Choe Ra Mi Cha Song-Yi Kim Bang-Hun Hyun Bong-Kyun Park Dong-Jun An Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars Pathogens PCV2 wild boar recombination tMRCA genotype shift |
| title | Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars |
| title_full | Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars |
| title_fullStr | Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars |
| title_full_unstemmed | Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars |
| title_short | Genetic Diversity of Porcine Circovirus Isolated from Korean Wild Boars |
| title_sort | genetic diversity of porcine circovirus isolated from korean wild boars |
| topic | PCV2 wild boar recombination tMRCA genotype shift |
| url | https://www.mdpi.com/2076-0817/9/6/457 |
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