Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020
ABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV) poses an extensive economic threat to the United States swine industry. The high degree of PRRSV genetic and antigenic variability challenges existing vaccination programs. We evaluated the ORF5 sequence of 1,931 PRRSV-2 strains de...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-06-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.02634-21 |
| _version_ | 1818218459696201728 |
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| author | Ruwini Rupasinghe Kyuyoung Lee Xin Liu Phillip C. Gauger Jianqiang Zhang Beatriz Martínez-López |
| author_facet | Ruwini Rupasinghe Kyuyoung Lee Xin Liu Phillip C. Gauger Jianqiang Zhang Beatriz Martínez-López |
| author_sort | Ruwini Rupasinghe |
| collection | DOAJ |
| description | ABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV) poses an extensive economic threat to the United States swine industry. The high degree of PRRSV genetic and antigenic variability challenges existing vaccination programs. We evaluated the ORF5 sequence of 1,931 PRRSV-2 strains detected from >300 farms managed by two pork production systems in the midwestern United States from 2001 to 2020 to assess the genetic diversity and molecular characteristics of heterologous PRRSV-2 strains. Phylogenetic analysis was performed on ORF5 sequences and classified using the global PRRSV classification system. N-glycosylation and the global and local selection pressure in the putative GP5 encoded by ORF5 were estimated. The PRRSV-2 sequences were classified into lineage 5 (L5; n = 438[22.7%]) or lineage 1 (L1; n = 1,493[77.3%]). The L1 strains belonged to one of three subclades: L1A (n = 1,225[63.4%]), L1B (n = 69[3.6%]), and L1C/D (n = 199[10.3%]). 10 N-glycosylation sites were predicted, and positions N44 and N51 were detected in most GP5 sequences (n = 1,801[93.3%]). Clade-specific N-glycosylation sites were observed: 57th in L1A, 33rd in L1B, 30th and 34th in L1C/D, and 30th and 33rd in L5. We identified nine and 19 sites in GP5 under significant positive selection in L5 and L1, respectively. The 13th, 151st, and 200th positive selection sites were exclusive to L5. Heterogeneity of N-glycosylation and positive selection sites may contribute to varying the evolutionary processes of PRRSV-2 strains circulating in these swine production systems. L1A and L5 strains denoted excellence in adaptation to the current swine population by their extensive positive selection sites with higher site-specific selection pressure. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) is known for its high genetic and antigenic variability. In this study, we evaluated the ORF5 sequences of PRRSV-2 strains circulating in two swine production systems in the midwestern United States from 2001 to 2020. All the field strains were classified into four major groups based on genetic relatedness, where one group is closely related to the Ingelvac PRRS MLV strain. Here, we systematically compared differences in the ORF5 polymorphisms, N-glycosylation sites, and local and global evolutionary dynamics between different groups. Sites 44 and 51 were common for N-glycosylation in most amino acid sequences (n = 1,801, 93.3%). We identified that the L5 sequences had more positive selection pressure compared to the L1 strains. Our findings will provide valuable insights into the evolutionary mechanisms of PRRSV-2 and these molecular changes may lead to suboptimal effectiveness of Ingelvac PRRS MLV vaccine. |
| first_indexed | 2024-12-12T07:24:06Z |
| format | Article |
| id | doaj.art-c5fb635c82e24192bef01a0bddc8c95c |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-12-12T07:24:06Z |
| publishDate | 2022-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-c5fb635c82e24192bef01a0bddc8c95c2022-12-22T00:33:12ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-06-0110310.1128/spectrum.02634-21Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020Ruwini Rupasinghe0Kyuyoung Lee1Xin Liu2Phillip C. Gauger3Jianqiang Zhang4Beatriz Martínez-López5Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USACenter for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USADepartment of Computer Science, University of California, Davis, California, USADepartment of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USADepartment of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USACenter for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USAABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV) poses an extensive economic threat to the United States swine industry. The high degree of PRRSV genetic and antigenic variability challenges existing vaccination programs. We evaluated the ORF5 sequence of 1,931 PRRSV-2 strains detected from >300 farms managed by two pork production systems in the midwestern United States from 2001 to 2020 to assess the genetic diversity and molecular characteristics of heterologous PRRSV-2 strains. Phylogenetic analysis was performed on ORF5 sequences and classified using the global PRRSV classification system. N-glycosylation and the global and local selection pressure in the putative GP5 encoded by ORF5 were estimated. The PRRSV-2 sequences were classified into lineage 5 (L5; n = 438[22.7%]) or lineage 1 (L1; n = 1,493[77.3%]). The L1 strains belonged to one of three subclades: L1A (n = 1,225[63.4%]), L1B (n = 69[3.6%]), and L1C/D (n = 199[10.3%]). 10 N-glycosylation sites were predicted, and positions N44 and N51 were detected in most GP5 sequences (n = 1,801[93.3%]). Clade-specific N-glycosylation sites were observed: 57th in L1A, 33rd in L1B, 30th and 34th in L1C/D, and 30th and 33rd in L5. We identified nine and 19 sites in GP5 under significant positive selection in L5 and L1, respectively. The 13th, 151st, and 200th positive selection sites were exclusive to L5. Heterogeneity of N-glycosylation and positive selection sites may contribute to varying the evolutionary processes of PRRSV-2 strains circulating in these swine production systems. L1A and L5 strains denoted excellence in adaptation to the current swine population by their extensive positive selection sites with higher site-specific selection pressure. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) is known for its high genetic and antigenic variability. In this study, we evaluated the ORF5 sequences of PRRSV-2 strains circulating in two swine production systems in the midwestern United States from 2001 to 2020. All the field strains were classified into four major groups based on genetic relatedness, where one group is closely related to the Ingelvac PRRS MLV strain. Here, we systematically compared differences in the ORF5 polymorphisms, N-glycosylation sites, and local and global evolutionary dynamics between different groups. Sites 44 and 51 were common for N-glycosylation in most amino acid sequences (n = 1,801, 93.3%). We identified that the L5 sequences had more positive selection pressure compared to the L1 strains. Our findings will provide valuable insights into the evolutionary mechanisms of PRRSV-2 and these molecular changes may lead to suboptimal effectiveness of Ingelvac PRRS MLV vaccine.https://journals.asm.org/doi/10.1128/spectrum.02634-21PRRSV-2wild-typeMLVRFLPN-glycosylationselection pressure |
| spellingShingle | Ruwini Rupasinghe Kyuyoung Lee Xin Liu Phillip C. Gauger Jianqiang Zhang Beatriz Martínez-López Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020 Microbiology Spectrum PRRSV-2 wild-type MLV RFLP N-glycosylation selection pressure |
| title | Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020 |
| title_full | Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020 |
| title_fullStr | Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020 |
| title_full_unstemmed | Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020 |
| title_short | Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020 |
| title_sort | molecular evolution of porcine reproductive and respiratory syndrome virus field strains from two swine production systems in the midwestern united states from 2001 to 2020 |
| topic | PRRSV-2 wild-type MLV RFLP N-glycosylation selection pressure |
| url | https://journals.asm.org/doi/10.1128/spectrum.02634-21 |
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