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Shen YF, Arruda AG, Koscielny MP, Cheng TY. Contrasting PRRSV temporal lineage patterns at the individual farm, production system, and regional levels in Ohio and neighboring states from 2017 to 2021. Prev Vet Med 2024; 226:106186. [PMID: 38518657 DOI: 10.1016/j.prevetmed.2024.106186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/13/2024] [Accepted: 03/13/2024] [Indexed: 03/24/2024]
Abstract
Porcine reproductive and respiratory virus (PRRSV), one of the most significant viruses in the swine industry, has been challenging to control due to its high mutation and recombination rates and complexity. This retrospective study aimed to describe and compare the distribution of PRRSV lineages obtained at the individual farm, production system, and regional levels. PRRSV-2 (type 2) sequences (n = 482) identified between 2017 - 2021 were provided by a regional state laboratory (Ohio Department of Agriculture, Animal Disease Diagnostic Center (ODA-ADDL)) collected from swine farms in Ohio and neighboring states, including Indiana, Michigan, Pennsylvania, and West Virginia. Additional sequences (n = 138) were provided by one collaborating swine production system. The MUSCLE algorithm on Geneious Prime® was used to align the ORF5 region of PRRSV-2 sequences along with PRRSV live attenuated vaccine strains (n = 6) and lineage anchors (n = 169). Sequenced PRRSV-2 were assigned to the most identical lineage anchors/vaccine strains. Among all sequences (n = 620), 29.8% (185/620) were ≥ 98.0% identity with the vaccine strains, where 93.5% (173/185) and 6.5% (12/185) were identical with the L5 Ingelvac PRRS® MLV and L8 Fostera® PRRS vaccine strains, respectively, and excluded from the analysis. At the regional level across five years, the top five most identified lineages included L1A, L5, L1H, L1C, and L8. Among non-vaccine sequences with production system known, L1A sequences were mostly identified (64.3% - 100.0%) in five systems, followed by L1H (0.0% - 28.6%), L1C (0.0% - 10.5%), L5 (0.0% - 14.4%), L8 (0.0% - 1.3%), and L1F (0.0% - 0.5%). Furthermore, among non-vaccine sequences with the premise identification available (n = 262), the majority of sequences from five individual farms were either classified into L1A or L5. L1A and L5 sequences coexisted in three farms, while samples submitted by one farm contained L1A, L1H, and L5 sequences. Additionally, the lineage classification results of non-vaccine sequences were associated with their restriction fragment length polymorphism (RFLP) patterns (Fisher's exact test, p < 0.05). Overall, our results show that individual farm and production system-level PRRSV-2 lineage patterns do not necessarily correspond to regional-level patterns, highlighting the influence of individual farms and systems in shaping PRRSV occurrence within those levels, and highlighting the crucial goal of within-farm and system monitoring and early detection for accurate knowledge on PRRSV-2 lineage occurrence and emergence.
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Affiliation(s)
- Yi-Fan Shen
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Andréia G Arruda
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
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Yim-im W, Anderson TK, Paploski IAD, VanderWaal K, Gauger P, Krueger K, Shi M, Main R, Zhang J. Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes. Microbiol Spectr 2023; 11:e0291623. [PMID: 37933982 PMCID: PMC10848785 DOI: 10.1128/spectrum.02916-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/01/2023] [Indexed: 11/08/2023] Open
Abstract
IMPORTANCE In this study, comprehensive analysis of 82,237 global porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) open reading frame 5 sequences spanning from 1989 to 2021 refined PRRSV-2 genetic classification system, which defines 11 lineages and 21 sublineages and provides flexibility for growth if additional lineages, sublineages, or more granular classifications are needed in the future. Geographic distribution and temporal changes of PRRSV-2 were investigated in detail. This is a thorough study describing the molecular epidemiology of global PRRSV-2. In addition, the reference sequences based on the refined genetic classification system are made available to the public for future epidemiological and diagnostic applications worldwide. The data from this study will facilitate global standardization and application of PRRSV-2 genetic classification.
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Affiliation(s)
- Wannarat Yim-im
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Igor A. D. Paploski
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Phillip Gauger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Karen Krueger
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Mang Shi
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Rodger Main
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Jianqiang Zhang
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Li C, Gong B, Sun Q, Xu H, Zhao J, Xiang L, Tang YD, Leng C, Li W, Guo Z, Fu J, Peng J, Wang Q, Zhou G, Yu Y, Meng F, An T, Cai X, Tian ZJ, Zhang H. First Detection of NADC34-like PRRSV as a Main Epidemic Strain on a Large Farm in China. Pathogens 2021; 11:pathogens11010032. [PMID: 35055980 PMCID: PMC8778757 DOI: 10.3390/pathogens11010032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
The newly emerged sublineage 1.5 (NADC34-like) porcine reproductive and respiratory syndrome virus (PRRSV) has posed a direct threat to the Chinese pig industry since 2018. However, the prevalence and impact of NADC34-like PRRSV on Chinese pig farms is unclear. In the present study, we continuously monitored pathogens—including PRRSV, African swine fever virus (ASFV), classical swine fever virus (CSFV), pseudorabies virus (PRV), and porcine circovirus 2 (PCV2)—on a fattening pig farm with strict biosecurity practices located in Heilongjiang Province, China, from 2020 to 2021. The results showed that multiple types of PRRSV coexisted on a single pig farm. NADC30-like and NADC34-like PRRSVs were the predominant strains on this pig farm. Importantly, NADC34-like PRRSV—detected during the period of peak mortality—was one of the predominant strains on this pig farm. Sequence alignment suggested that these strains shared the same 100 aa deletion in the NSP2 protein as IA/2014/NADC34 isolated from the United States (U.S.) in 2014. Phylogenetic analysis based on open reading frame 5 (ORF5) showed that the genetic diversity of NADC34-like PRRSV on this farm was relatively singular, but it had a relatively high rate of evolution. Restriction fragment length polymorphism (RFLP) pattern analysis showed that almost all ORF5 RFLPs were 1-7-4, with one 1-4-4. In addition, two complete genomes of NADC34-like PRRSVs were sequenced. Recombination analysis and sequence alignment demonstrated that both viruses, with 98.9% nucleotide similarity, were non-recombinant viruses. This study reports the prevalence and characteristics of NADC34-like PRRSVs on a large-scale breeding farm in northern China for the first time. These results will help to reveal the impact of NADC34-like PRRSVs on Chinese pig farms, and provide a reference for the detection and further prevention and control of NADC34-like PRRSVs.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Bangjun Gong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Qi Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Hu Xu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jing Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Lirun Xiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Chaoliang Leng
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan Provincial Engineering Laboratory of Insects Bio-Reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, China;
| | - Wansheng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Zhenyang Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jun Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jinmei Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Qian Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Guohui Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Ying Yu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fandan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Hongliang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
- Correspondence: ; Tel.: +86-13624503578
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Papatsiros V, Stylianaki I, Papakonstantinou G, Tsekouras N, Bitchava D, Christodoulopoulos G, Papaioannou N. Histopathological Lesions Accompanied with First-Time Isolation of a PRRSV-2 Strain in Greece. Viral Immunol 2020; 33:565-570. [PMID: 33001795 DOI: 10.1089/vim.2020.0087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genotype 2 strains of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV-2) have been reported sporadically in Europe. Even if, PRRSV-2 reported to be genetically homogenous in Europe due to the introduction of an MLV vaccine strain, independent introductions of PRRSV-2 field strains have been reported. The aim of the present study was to report the complete genome sequence and evaluate the histopathological lesions of a PRRSV-2 strain, isolated for the first time in Greece. During a routine blood sampling in a commercial pig farm, the results revealed positive samples in weaners of 40-60 days for the PRRSV-2, using real-time polymerase chain reaction. The clinical picture was characterized from respiratory symptoms in weaners, as well as coughing and poor performance at finishing stage and less than 3% mortality rate from weaning stage to finishing stage. The use of ORF5 for PRRSV phylogenetic analysis of the isolated PRRSV strain, named "x1544-1 strain", was successfully determined, belonging to the genotype PRRSV-2. Comparison of the obtained sequence revealed nucleotide sequence identity >98% with PRRSV-2 strain VR2332 and other related strains from Denmark and China. The histopathological evaluation revealed diffuse interstitial pneumonia, multifocal interstitial nephritis, while in the lymphoid organs, follicular and paracortical hyperplasia, coexisting with necrosis and depletion of germ cells were detected. The results of current study undersign the importance for veterinary practitioners to have up-to-date access to phylogenetic data linked to phenotypic information to follow-up the control and prevention strategies against PRRSV.
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Affiliation(s)
- Vasileios Papatsiros
- Clinic of Medicine, Faculty of Veterinary Medicine, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Ioanna Stylianaki
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Papakonstantinou
- Clinic of Medicine, Faculty of Veterinary Medicine, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Nikolaos Tsekouras
- Clinic of Medicine, Faculty of Veterinary Medicine, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | | | - Georgios Christodoulopoulos
- Clinic of Medicine, Faculty of Veterinary Medicine, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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5
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Lambert MÈ, Delisle B, Arsenault J, Poljak Z, D'Allaire S. Positioning Quebec ORF5 sequences of porcine reproductive and respiratory syndrome virus (PRRSV) within Canada and worldwide diversity. INFECTION GENETICS AND EVOLUTION 2019; 74:103999. [PMID: 31408766 DOI: 10.1016/j.meegid.2019.103999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 01/13/2023]
Abstract
Sequencing of ORF5 gene is widely used and considered essential for diagnostics and control of porcine reproductive and respiratory syndrome (PRRS) in Canada. The objective of this study was to position Quebec ORF5 sequences of PRRS virus within Canada and worldwide diversity. Overall, 76.8% of the 5204 sequences gathered from Quebec (n = 5031), Ontario (n = 151) and Manitoba (n = 18) were classified into one of 34 genetic clusters defined as groupings including ≥15 sequences and having ≥70% rapid bootstrap support value from a maximum likelihood (ML)-phylogeny. Following the addition of PRRSV 2 international reference dataset from Shi et al. (2010), the most predominant lineages in our dataset were wild-type 1 and vaccine-like 5.1 (MLV) and 8.9 (ATP). No strains or only a very few (1 or 2) were assigned to lineages 1.3-1.5, 3, 4, 5.2, 6, 7 or 9. Most wild-type clusters (97%) detected in a dataset from Canada did not include any sequence from the international reference dataset. It might reflect recent subpopulations that were absent at the time of Shi's publication. As an example, cluster #25 first appeared in 2007, but since then had expanded considerably and is now the most prevalent wild-type cluster found in Quebec. A total of 117 RFLP patterns were identified and those were poorly correlated with genetic clusters based on phylogeny. Factors modulating PRRSV diversity such as pig movement that occurred within and between provinces should be further investigated in a perspective of disease control.
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Affiliation(s)
- Marie-Ève Lambert
- Laboratoire d'épidémiologie et de médecine porcine (LEMP), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada.
| | - Benjamin Delisle
- Laboratoire d'épidémiologie et de médecine porcine (LEMP), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada
| | - Julie Arsenault
- Laboratoire d'épidémiologie et de médecine porcine (LEMP), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | - Sylvie D'Allaire
- Laboratoire d'épidémiologie et de médecine porcine (LEMP), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, Université de Montréal, St. Hyacinthe, Quebec, Canada
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6
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Evaluating an automated clustering approach in a perspective of ongoing surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) field strains. INFECTION GENETICS AND EVOLUTION 2019; 73:295-305. [PMID: 31039449 DOI: 10.1016/j.meegid.2019.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/06/2019] [Accepted: 04/18/2019] [Indexed: 01/13/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) has a major economic impact on the swine industry. The important genetic diversity needs to be considered for disease management. In this regard, information on the circulating endemic strains and their dispersal patterns through ongoing surveillance is beneficial. The objective of this project was to classify Quebec PRRSV ORF5 sequences in genetic clusters and evaluate stability of clustering results over a three-year period using an in-house automated clustering system. Phylogeny based on maximum likelihood (ML) was first inferred on 3661 sequences collected in 1998-2013 (Run 1). Then, sequences collected between January 2014 and September 2016 were sequentially added into 11 consecutive runs, each one covering a three-month period. For each run, detection of clusters, which were defined as groups of ≥15 sequences having a≥70% rapid bootstrap support (RBS) value, was automated in Python. Cluster stability was described for each cluster and run based on the number of sequences, RBS value, maximum pairwise distance and agreement in sequence assignment to a specific cluster. First and last run identified 29 and 33 clusters, respectively. In the last run, about 77% of the sequences were classified by the system. Most clusters were stable through time, with sequences attributed to one cluster in Run 1 staying in the same cluster for the 11 remaining runs. However, some initial groups were further subdivided into subgroups with time, which is important for monitoring since one specific wild-type cluster increased from 0% in 2007 to 45% of all sequences in 2016. This automated classification system will be integrated into ongoing surveillance activities, to facilitate communication and decision-making for stakeholders of the swine industry.
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7
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Diseases Primarily Affecting the Reproductive System. Vet Med (Auckl) 2017. [PMCID: PMC7150237 DOI: 10.1016/b978-0-7020-5246-0.00018-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Perez AM, Davies PR, Goodell CK, Holtkamp DJ, Mondaca-Fernández E, Poljak Z, Tousignant SJ, Valdes-Donoso P, Zimmerman JJ, Morrison RB. Lessons learned and knowledge gaps about the epidemiology and control of porcine reproductive and respiratory syndrome virus in North America. J Am Vet Med Assoc 2016; 246:1304-17. [PMID: 26043128 DOI: 10.2460/javma.246.12.1304] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Wang X, Marthaler D, Rovira A, Rossow S, Murtaugh MP. Emergence of a virulent porcine reproductive and respiratory syndrome virus in vaccinated herds in the United States. Virus Res 2015; 210:34-41. [DOI: 10.1016/j.virusres.2015.07.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
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10
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Brar MS, Murtaugh MP, Shi M, Leung FCC. Evolutionary diversification of type 2 porcine reproductive and respiratory syndrome virus. J Gen Virol 2015; 96:1570-80. [DOI: 10.1099/vir.0.000104] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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11
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Balka G, Wang X, Olasz F, Bálint Á, Kiss I, Bányai K, Rusvai M, Stadejek T, Marthaler D, Murtaugh MP, Zádori Z. Full genome sequence analysis of a wild, non-MLV-related type 2 Hungarian PRRSV variant isolated in Europe. Virus Res 2015; 200:1-8. [PMID: 25616050 DOI: 10.1016/j.virusres.2015.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 11/15/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a widespread pathogen of pigs causing significant economic losses to the swine industry. The expanding diversity of PRRSV strains makes the diagnosis, control and eradication of the disease more and more difficult. In the present study, the authors report the full genome sequencing of a type 2 PRRSV strain isolated from piglet carcasses in Hungary. Next generation sequencing was used to determine the complete genome sequence of the isolate (PRRSV-2/Hungary/102/2012). Recombination analysis performed with the available full-length genome sequences showed no evidence of such event with other known PRRSV. Unique deletions and an insertion were found in the nsp2 region of PRRSV-2/Hungary/102/2012 when it was compared to the highly virulent VR2332 and JXA-1 prototype strains. The majority of amino acid alterations in GP4 and GP5 of the virus were in the known antigenic regions suggesting an important role for immunological pressure in PRRSV-2/Hungary/102/2012 evolution. Phylogenetic analysis revealed that it belongs to lineage 1 or 2 of type 2 PRRSV. Considering the lack of related PRRSV in Europe, except for a partial sequence from Slovakia, the ancestor of PRRSV-2/Hungary/102/2012 was most probably transported from North-America. It is the first documented type 2 PRRSV isolated in Europe that is not related to the Ingelvac MLV.
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Affiliation(s)
- Gyula Balka
- Department of Pathology, Faculty of Veterinary Science, Szent István University, István u. 2, H-1078 Budapest, Hungary.
| | - Xiong Wang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA
| | - Ferenc Olasz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Ádám Bálint
- National Food Chain Safety Office Veterinary Diagnostic Directorate, Tábornok u. 2, H-1143 Budapest, Hungary
| | - István Kiss
- Ceva-Phylaxia Veterinary Biologicals Co. Ltd., Szállás u. 5, H-1107 Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Miklós Rusvai
- Department of Pathology, Faculty of Veterinary Science, Szent István University, István u. 2, H-1078 Budapest, Hungary
| | - Tomasz Stadejek
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, ul. Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Douglas Marthaler
- Veterinary Diagnostic Laboratory, University of Minnesota, 1333 Gortner Avenue, St. Paul, MN 55108, USA
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
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Shi M, Lemey P, Singh Brar M, Suchard MA, Murtaugh MP, Carman S, D'Allaire S, Delisle B, Lambert MÈ, Gagnon CA, Ge L, Qu Y, Yoo D, Holmes EC, Chi-Ching Leung F. The spread of type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: a phylogeographic approach. Virology 2013; 447:146-54. [PMID: 24210109 DOI: 10.1016/j.virol.2013.08.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 08/23/2013] [Accepted: 08/23/2013] [Indexed: 11/17/2022]
Abstract
The emergence and spread of Type 2 Porcine Reproductive and Respiratory Syndrome virus (Type 2 PRRSV) in North America is heavily influenced by the multiple site production system used in the hog industry. However, it is unclear how anthropogenic factors such has this have shaped the current spatial distribution of PRRSV genotypes. We employed Bayesian phylogeographic analyses of 7040 ORF5 sequences to reveal the recent geographical spread of Type 2 PRRSV in North America. The directions and intensities in our inferred virus traffic network closely mirror the hog transportation. Most notably, we reveal multiple viral introductions from Canada into the United States causing a major shift in virus genetic composition in the Midwest USA that went unnoticed by the regular surveillance and field epidemiological studies. Overall, these findings provide important insights into the dynamics of Type 2 PRRSV evolution and spread that will facilitate programs for control and prevention.
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Affiliation(s)
- Mang Shi
- Sydney Emerging Infections & Biosecurity Institute, School of Biological Sciences and Sydney Medical School, The University of Sydney, NSW 2006, Australia
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13
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Stadejek T, Stankevicius A, Murtaugh MP, Oleksiewicz MB. Molecular evolution of PRRSV in Europe: current state of play. Vet Microbiol 2013; 165:21-8. [PMID: 23528651 DOI: 10.1016/j.vetmic.2013.02.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 02/22/2013] [Accepted: 02/27/2013] [Indexed: 11/18/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to European swine production. The existence of extensive genetic variation in endemic strains and the presence of highly virulent strains in other geographic regions pose the threat of devastating epidemic outbreaks. Here we describe the current knowledge of genetic variation in European PRRSV isolates, the implications for PRRSV evolution, and the presence of multiple genetic lineages of Type 2 (North American genotype) isolates in Europe. In Type 1 (European genotype) PRRSV, three genetic subtypes are recognized and a fourth subtype appears to be present. Type 2 PRRSV was considered to be genetically homogenous in Europe due to a unique presence of an introduced vaccine strain, but independent introductions of virulent Type 2 field viruses are now evident. In Type 1 PRRSV, only subtype 1 (Lelystad virus-like) circulates in Central and Western Europe and globally. In Eastern Europe, all subtypes are present. The subtypes of Type 1 PRRSV also exhibit length differences in the nucleocapsid protein, ranging in size from 124 to 132 amino acids depending on subtype. This size heterogeneity is unparalleled in the nucleocapsid proteins of Type 2 PRRSV or other viruses. Surprisingly, it affects the C-terminus, otherwise thought to be under strong structural constraints. Finally, divergent subtypes of Type 1 PRRSV have produced high rates of false-negative RT-PCR results in diagnostic tests, and may also degrade the reliability of serodiagnostic assays using the nucleocapsid protein antigen. In summary, the extensive genetic diversity of Type 1 PRRSV is of relevance for understanding nucleocapsid protein structure/function relationships. Further, the extensive genetic diversity of Type 1 PRRSV in Europe, and the presence of diverse Type 2 PRRSV strains, together emphasize the importance of relevant validation of PRRSV diagnostics. More extensive and systematic molecular phylogeny studies are needed to fully understand PRRSV diversity in Europe, to provide swine producers with reliable diagnostics, and to better assess the potential consequences of endemic spread and exotic introductions.
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Affiliation(s)
- Tomasz Stadejek
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland.
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