Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea
Abstract Background Porcine reproductive and respiratory syndrome virus (PRRSV) is a macrophage-tropic arterivirus with extremely high genetic and pathogenic heterogeneity that causes significant economic losses in the swine industry worldwide. PRRSV can be divided into two species [PRRSV1 (European...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-022-01790-6 |
| _version_ | 1818273518109851648 |
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| author | Seung-Chai Kim Sung-Hyun Moon Chang-Gi Jeong Gyeong-Seo Park Ji-Young Park Hye-Young Jeoung Go-Eun Shin Mi-Kyeong Ko Seoung-Hee Kim Kyoung-Ki Lee Ho-Seong Cho Won-Il Kim |
| author_facet | Seung-Chai Kim Sung-Hyun Moon Chang-Gi Jeong Gyeong-Seo Park Ji-Young Park Hye-Young Jeoung Go-Eun Shin Mi-Kyeong Ko Seoung-Hee Kim Kyoung-Ki Lee Ho-Seong Cho Won-Il Kim |
| author_sort | Seung-Chai Kim |
| collection | DOAJ |
| description | Abstract Background Porcine reproductive and respiratory syndrome virus (PRRSV) is a macrophage-tropic arterivirus with extremely high genetic and pathogenic heterogeneity that causes significant economic losses in the swine industry worldwide. PRRSV can be divided into two species [PRRSV1 (European) and PRRSV2 (North American)] and is usually diagnosed and genetically differentiated into several lineages based on the ORF5 gene, which constitutes only 5% of the whole genome. This study was conducted to achieve nonselective amplification and whole-genome sequencing (WGS) based on a simplified sequence-independent, single-primer amplification (SISPA) technique with next-generation sequencing (NGS), and to genetically characterize Korean PRRSV field isolates at the whole genome level. Methods The SISPA-NGS method coupled with a bioinformatics pipeline was utilized to retrieve full length PRRSV genomes of 19 representative Korean PRRSV strains by de novo assembly. Phylogenetic analysis, analysis of the insertion and deletion (INDEL) pattern of nonstructural protein 2 (NSP2), and recombination analysis were conducted. Results Nineteen complete PRRSV genomes were obtained with a high depth of coverage by the SISPA-NGS method. Korean PRRSV1 belonged to the Korean-specific subtype 1A and vaccine-related subtype 1C lineages, showing no evidence of recombination and divergent genetic heterogeneity with conserved NSP2 deletion patterns. Among Korean PRRSV2 isolates, modified live vaccine (MLV)-related lineage 5 viruses, lineage 1 viruses, and nation-specific Korean lineages (KOR A, B and C) could be identified. The NSP2 deletion pattern of the Korean lineages was consistent with that of the MN-184 strain (lineage 1), which indicates the common ancestor and independent evolution of Korean lineages. Multiple recombination signals were detected from Korean-lineage strains isolated in the 2010s, suggesting natural interlineage recombination between circulating KOR C and MLV strains. Interestingly, the Korean strain GGYC45 was identified as a recombinant KOR C and MLV strain harboring the KOR B ORF5 gene and might be the ancestor of currently circulating KOR B strains. Additionally, two novel lineage 1 recombinants of NADC30-like and NADC34-like viruses were detected. Conclusion Genome-wide analysis of Korean PRRSV isolates retrieved by the SISPA-NGS method and de novo assembly, revealed complex evolution and recombination in the field. Therefore, continuous surveillance of PRRSV at the whole genome level should be conducted, and new vaccine strategies for more efficient control of the virus are needed. |
| first_indexed | 2024-12-12T21:59:14Z |
| format | Article |
| id | doaj.art-e065cfee8c9e430dac340a5b8c059790 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-12T21:59:14Z |
| publishDate | 2022-04-01 |
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| series | Virology Journal |
| spelling | doaj.art-e065cfee8c9e430dac340a5b8c0597902022-12-22T00:10:34ZengBMCVirology Journal1743-422X2022-04-0119111310.1186/s12985-022-01790-6Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in KoreaSeung-Chai Kim0Sung-Hyun Moon1Chang-Gi Jeong2Gyeong-Seo Park3Ji-Young Park4Hye-Young Jeoung5Go-Eun Shin6Mi-Kyeong Ko7Seoung-Hee Kim8Kyoung-Ki Lee9Ho-Seong Cho10Won-Il Kim11College of Veterinary Medicine, Jeonbuk National UniversityCollege of Veterinary Medicine, Jeonbuk National UniversityCollege of Veterinary Medicine, Jeonbuk National UniversityCollege of Veterinary Medicine, Jeonbuk National UniversityAnimal and Plant Quarantine AgencyAnimal and Plant Quarantine AgencyAnimal and Plant Quarantine AgencyAnimal and Plant Quarantine AgencyAnimal and Plant Quarantine AgencyAnimal and Plant Quarantine AgencyCollege of Veterinary Medicine, Jeonbuk National UniversityCollege of Veterinary Medicine, Jeonbuk National UniversityAbstract Background Porcine reproductive and respiratory syndrome virus (PRRSV) is a macrophage-tropic arterivirus with extremely high genetic and pathogenic heterogeneity that causes significant economic losses in the swine industry worldwide. PRRSV can be divided into two species [PRRSV1 (European) and PRRSV2 (North American)] and is usually diagnosed and genetically differentiated into several lineages based on the ORF5 gene, which constitutes only 5% of the whole genome. This study was conducted to achieve nonselective amplification and whole-genome sequencing (WGS) based on a simplified sequence-independent, single-primer amplification (SISPA) technique with next-generation sequencing (NGS), and to genetically characterize Korean PRRSV field isolates at the whole genome level. Methods The SISPA-NGS method coupled with a bioinformatics pipeline was utilized to retrieve full length PRRSV genomes of 19 representative Korean PRRSV strains by de novo assembly. Phylogenetic analysis, analysis of the insertion and deletion (INDEL) pattern of nonstructural protein 2 (NSP2), and recombination analysis were conducted. Results Nineteen complete PRRSV genomes were obtained with a high depth of coverage by the SISPA-NGS method. Korean PRRSV1 belonged to the Korean-specific subtype 1A and vaccine-related subtype 1C lineages, showing no evidence of recombination and divergent genetic heterogeneity with conserved NSP2 deletion patterns. Among Korean PRRSV2 isolates, modified live vaccine (MLV)-related lineage 5 viruses, lineage 1 viruses, and nation-specific Korean lineages (KOR A, B and C) could be identified. The NSP2 deletion pattern of the Korean lineages was consistent with that of the MN-184 strain (lineage 1), which indicates the common ancestor and independent evolution of Korean lineages. Multiple recombination signals were detected from Korean-lineage strains isolated in the 2010s, suggesting natural interlineage recombination between circulating KOR C and MLV strains. Interestingly, the Korean strain GGYC45 was identified as a recombinant KOR C and MLV strain harboring the KOR B ORF5 gene and might be the ancestor of currently circulating KOR B strains. Additionally, two novel lineage 1 recombinants of NADC30-like and NADC34-like viruses were detected. Conclusion Genome-wide analysis of Korean PRRSV isolates retrieved by the SISPA-NGS method and de novo assembly, revealed complex evolution and recombination in the field. Therefore, continuous surveillance of PRRSV at the whole genome level should be conducted, and new vaccine strategies for more efficient control of the virus are needed.https://doi.org/10.1186/s12985-022-01790-6Genetic diversityPorcine reproductive and respiratory syndrome virus (PRRSV)RecombinationPhylogenetic analysisEvolution |
| spellingShingle | Seung-Chai Kim Sung-Hyun Moon Chang-Gi Jeong Gyeong-Seo Park Ji-Young Park Hye-Young Jeoung Go-Eun Shin Mi-Kyeong Ko Seoung-Hee Kim Kyoung-Ki Lee Ho-Seong Cho Won-Il Kim Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea Virology Journal Genetic diversity Porcine reproductive and respiratory syndrome virus (PRRSV) Recombination Phylogenetic analysis Evolution |
| title | Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea |
| title_full | Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea |
| title_fullStr | Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea |
| title_full_unstemmed | Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea |
| title_short | Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea |
| title_sort | whole genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus prrsv isolates in korea |
| topic | Genetic diversity Porcine reproductive and respiratory syndrome virus (PRRSV) Recombination Phylogenetic analysis Evolution |
| url | https://doi.org/10.1186/s12985-022-01790-6 |
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