WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study
Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of one of the most widespread and economically devastating diseases in the swine industry. Typing circulating PRRSV strains by means of sequencing is crucial for developing adequate control strategies. Most genetic st...
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| Format: | Article |
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MDPI AG
2021-12-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/12/2419 |
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| author | Frank Vandenbussche Elisabeth Mathijs Marylène Tignon Tamara Vandersmissen Ann Brigitte Cay |
| author_facet | Frank Vandenbussche Elisabeth Mathijs Marylène Tignon Tamara Vandersmissen Ann Brigitte Cay |
| author_sort | Frank Vandenbussche |
| collection | DOAJ |
| description | Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of one of the most widespread and economically devastating diseases in the swine industry. Typing circulating PRRSV strains by means of sequencing is crucial for developing adequate control strategies. Most genetic studies only target the highly variable open reading frame (ORF) 5, for which an extensive database is available. In this study, we performed whole-genome sequencing (WGS) on a collection of 124 PRRSV-1 positive serum samples that were collected over a 5-year period (2015–2019) in Belgium. Our results show that (nearly) complete PRRSV genomes can be obtained directly from serum samples with a high success rate. Analysis of the coding regions confirmed the exceptionally high genetic diversity, even among Belgian PRRSV-1 strains. To gain more insight into the added value of WGS, we performed phylogenetic cluster analyses on separate ORF datasets as well as on a single, concatenated dataset (CDS) containing all ORFs. A comparison between the CDS and ORF clustering schemes revealed numerous discrepancies. To explain these differences, we performed a large-scale recombination analysis, which allowed us to identify a large number of potential recombination events that were scattered across the genome. As PRRSV does not contain typical recombination hot-spots, typing PRRSV strains based on a single ORF is not recommended. Although the typing accuracy can be improved by including multiple regions, our results show that the full genetic diversity among PRRSV strains can only be captured by analysing (nearly) complete genomes. Finally, we also identified several vaccine-derived recombinant strains, which once more raises the question of the safety of these vaccines. |
| first_indexed | 2024-03-10T03:54:57Z |
| format | Article |
| id | doaj.art-38866dfe5e044c1f8072d088ff7ee767 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T03:54:57Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-38866dfe5e044c1f8072d088ff7ee7672023-11-23T10:57:40ZengMDPI AGViruses1999-49152021-12-011312241910.3390/v13122419WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case StudyFrank Vandenbussche0Elisabeth Mathijs1Marylène Tignon2Tamara Vandersmissen3Ann Brigitte Cay4Unit Exotic Viruses and Particular Diseases, Scientific Directorate of Infectious Diseases in Animals, Sciensano, 1180 Brussels, BelgiumUnit Enzootic, Vector-Borne and Bee Diseases, Scientific Directorate of Infectious Diseases in Animals, Sciensano, 1180 Brussels, BelgiumUnit Enzootic, Vector-Borne and Bee Diseases, Scientific Directorate of Infectious Diseases in Animals, Sciensano, 1180 Brussels, BelgiumAnimal Health Care Flanders (DGZ), 2500 Lier, BelgiumUnit Enzootic, Vector-Borne and Bee Diseases, Scientific Directorate of Infectious Diseases in Animals, Sciensano, 1180 Brussels, BelgiumPorcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of one of the most widespread and economically devastating diseases in the swine industry. Typing circulating PRRSV strains by means of sequencing is crucial for developing adequate control strategies. Most genetic studies only target the highly variable open reading frame (ORF) 5, for which an extensive database is available. In this study, we performed whole-genome sequencing (WGS) on a collection of 124 PRRSV-1 positive serum samples that were collected over a 5-year period (2015–2019) in Belgium. Our results show that (nearly) complete PRRSV genomes can be obtained directly from serum samples with a high success rate. Analysis of the coding regions confirmed the exceptionally high genetic diversity, even among Belgian PRRSV-1 strains. To gain more insight into the added value of WGS, we performed phylogenetic cluster analyses on separate ORF datasets as well as on a single, concatenated dataset (CDS) containing all ORFs. A comparison between the CDS and ORF clustering schemes revealed numerous discrepancies. To explain these differences, we performed a large-scale recombination analysis, which allowed us to identify a large number of potential recombination events that were scattered across the genome. As PRRSV does not contain typical recombination hot-spots, typing PRRSV strains based on a single ORF is not recommended. Although the typing accuracy can be improved by including multiple regions, our results show that the full genetic diversity among PRRSV strains can only be captured by analysing (nearly) complete genomes. Finally, we also identified several vaccine-derived recombinant strains, which once more raises the question of the safety of these vaccines.https://www.mdpi.com/1999-4915/13/12/2419porcine reproductive and respiratory syndrome viruswhole-genome sequencinggenotypingrecombination |
| spellingShingle | Frank Vandenbussche Elisabeth Mathijs Marylène Tignon Tamara Vandersmissen Ann Brigitte Cay WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study Viruses porcine reproductive and respiratory syndrome virus whole-genome sequencing genotyping recombination |
| title | WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study |
| title_full | WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study |
| title_fullStr | WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study |
| title_full_unstemmed | WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study |
| title_short | WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study |
| title_sort | wgs versus orf5 based typing of prrsv a belgian case study |
| topic | porcine reproductive and respiratory syndrome virus whole-genome sequencing genotyping recombination |
| url | https://www.mdpi.com/1999-4915/13/12/2419 |
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