PMID- 35410421 OWN - NLM STAT- MEDLINE DCOM- 20220413 LR - 20220606 IS - 1743-422X (Electronic) IS - 1743-422X (Linking) VI - 19 IP - 1 DP - 2022 Apr 11 TI - Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea. PG - 66 LID - 10.1186/s12985-022-01790-6 [doi] LID - 66 AB - 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. CI - (c) 2022. The Author(s). FAU - Kim, Seung-Chai AU - Kim SC AD - College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, Jeonbuk, 54596, Republic of Korea. FAU - Moon, Sung-Hyun AU - Moon SH AD - College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, Jeonbuk, 54596, Republic of Korea. FAU - Jeong, Chang-Gi AU - Jeong CG AD - College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, Jeonbuk, 54596, Republic of Korea. AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Park, Gyeong-Seo AU - Park GS AD - College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, Jeonbuk, 54596, Republic of Korea. FAU - Park, Ji-Young AU - Park JY AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Jeoung, Hye-Young AU - Jeoung HY AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Shin, Go-Eun AU - Shin GE AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Ko, Mi-Kyeong AU - Ko MK AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Kim, Seoung-Hee AU - Kim SH AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Lee, Kyoung-Ki AU - Lee KK AD - Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, 39660, Korea. FAU - Cho, Ho-Seong AU - Cho HS AD - College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, Jeonbuk, 54596, Republic of Korea. FAU - Kim, Won-Il AU - Kim WI AUID- ORCID: 0000-0002-0465-0794 AD - College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, Jeonbuk, 54596, Republic of Korea. kwi0621@jbnu.ac.kr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20220411 PL - England TA - Virol J JT - Virology journal JID - 101231645 SB - IM MH - Animals MH - Genome, Viral MH - Phylogeny MH - *Porcine Reproductive and Respiratory Syndrome/epidemiology MH - *Porcine respiratory and reproductive syndrome virus/genetics MH - Recombination, Genetic MH - Swine PMC - PMC8996673 OTO - NOTNLM OT - Evolution OT - Genetic diversity OT - Phylogenetic analysis OT - Porcine reproductive and respiratory syndrome virus (PRRSV) OT - Recombination COIS- The authors declare that they have no competing interests. EDAT- 2022/04/13 06:00 MHDA- 2022/04/14 06:00 PMCR- 2022/04/11 CRDT- 2022/04/12 05:22 PHST- 2021/09/28 00:00 [received] PHST- 2022/03/23 00:00 [accepted] PHST- 2022/04/12 05:22 [entrez] PHST- 2022/04/13 06:00 [pubmed] PHST- 2022/04/14 06:00 [medline] PHST- 2022/04/11 00:00 [pmc-release] AID - 10.1186/s12985-022-01790-6 [pii] AID - 1790 [pii] AID - 10.1186/s12985-022-01790-6 [doi] PST - epublish SO - Virol J. 2022 Apr 11;19(1):66. doi: 10.1186/s12985-022-01790-6.