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Walker LR, Vu HL, Montooth KL, Ciobanu DC. Functional and evolutionary analysis of host Synaptogyrin-2 in porcine circovirus type 2 susceptibility. PLoS Genet 2023; 19:e1011029. [PMID: 38011217 PMCID: PMC10703400 DOI: 10.1371/journal.pgen.1011029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/07/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023] Open
Abstract
Mammalian evolution has been influenced by viruses for millions of years, leaving signatures of adaptive evolution within genes encoding for viral interacting proteins. Synaptogyrin-2 (SYNGR2) is a transmembrane protein implicated in promoting bacterial and viral infections. A genome-wide association study of pigs experimentally infected with porcine circovirus type 2b (PCV2b) uncovered a missense mutation (SYNGR2 p.Arg63Cys) associated with viral load. In this study, CRISPR/Cas9-mediated gene editing of the porcine kidney 15 (PK15, wtSYNGR2+p.63Arg) cell line generated clones homozygous for the favorable SYNGR2 p.63Cys allele (emSYNGR2+p.63Cys). Infection of edited clones resulted in decreased PCV2 replication compared to wildtype PK15 (P<0.05), with consistent effects across genetically distinct PCV2b and PCV2d isolates. Sequence analyses of wild and domestic pigs (n>700) revealed the favorable SYNGR2 p.63Cys allele is unique to domestic pigs and more predominant in European than Asian breeds. A haplotype defined by the SYNGR2 p.63Cys allele was likely derived from an ancestral haplotype nearly fixed within European (0.977) but absent from Asian wild boar. We hypothesize that the SYNGR2 p.63Cys allele arose post-domestication in ancestral European swine. Decreased genetic diversity in homozygotes for the SYNGR2 p.63Cys allele compared to SYNGR2 p.63Arg, corroborates a rapid increase in frequency of SYGNR2 p.63Cys via positive selection. Signatures of adaptive evolution across mammalian species were also identified within SYNGR2 intraluminal loop domains, coinciding with the location of SYNGR2 p.Arg63Cys. Therefore, SYNGR2 may reflect a novel component of the host-virus evolutionary arms race across mammals with SYNGR2 p.Arg63Cys representing a species-specific example of putative adaptive evolution.
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Affiliation(s)
- Lianna R. Walker
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Hiep L. Vu
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Kristi L. Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Daniel C. Ciobanu
- Animal Science Department, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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Höltig D, Reiner G. [Opportunities and risks of the use of genetic resistances to infectious diseases in pigs - an overview]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2022; 50:46-58. [PMID: 35235982 DOI: 10.1055/a-1751-3531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Demands for health, performance and welfare in pigs, as well as the desire for consumer protection and reduced antibiotic use, require optimal measures in advance of disease development. This includes, in principle, the use of genetically more resistant lines and breeding animals, whose existence has been proven for a wide range of pathogen-host interactions. In addition, attempts are being made to identify the gene variants responsible for disease resistance in order to force the selection of suitable populations, also using modern biotechnical technics. The present work is intended to provide an overview of the research status achieved in this context and to highlight opportunities and risks for the future.The evaluation of the international literature shows that genetic disease resistance exist in many areas of swine diseases. However, polygenic inheritance, lack of animal models and the influence of environmental factors during evaluation render their implementation in practical breeding programs demanding. This is where modern molecular genetic methods, such as Gene Editing, come into play. Both approaches possess their pros and cons, which are discussed in this paper. The most important infectious diseases in pigs, including general diseases and epizootics, diseases of the respiratory and digestive tract and diseases of the immune system are taken into account.
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Affiliation(s)
- Doris Höltig
- Klinik für kleine Klauentiere, forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
| | - Gerald Reiner
- Klinikum Veterinärmedizin, Justus-Liebig-Universität
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Walker LR, Engle TB, Vu H, Tosky ER, Nonneman DJ, Smith TPL, Borza T, Burkey TE, Plastow GS, Kachman SD, Ciobanu DC. Synaptogyrin-2 influences replication of Porcine circovirus 2. PLoS Genet 2018; 14:e1007750. [PMID: 30379811 PMCID: PMC6245838 DOI: 10.1371/journal.pgen.1007750] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 11/20/2018] [Accepted: 10/09/2018] [Indexed: 11/19/2022] Open
Abstract
Porcine circovirus 2 (PCV2) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases (PCVAD). Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis. A large-scale genome-wide association study of experimentally infected pigs (n = 974), provided evidence of a host genetic role in PCV2 viremia, immune response and growth during challenge. Host genotype explained 64% of the phenotypic variation for overall viral load, with two major Quantitative Trait Loci (QTL) identified on chromosome 7 (SSC7) near the swine leukocyte antigen complex class II locus and on the proximal end of chromosome 12 (SSC12). The SNP having the strongest association, ALGA0110477 (SSC12), explained 9.3% of the genetic and 6.2% of the phenotypic variance for viral load. Dissection of the SSC12 QTL based on gene annotation, genomic and RNA-sequencing, suggested that a missense mutation in the SYNGR2 (SYNGR2 p.Arg63Cys) gene is potentially responsible for the variation in viremia. This polymorphism, located within a protein domain conserved across mammals, results in an amino acid variant SYNGR2 p.63Cys only observed in swine. PCV2 titer in PK15 cells decreased when the expression of SYNGR2 was silenced by specific-siRNA, indicating a role of SYNGR2 in viral replication. Additionally, a PK15 edited clone generated by CRISPR-Cas9, carrying a partial deletion of the second exon that harbors a key domain and the SYNGR2 p.Arg63Cys, was associated with a lower viral titer compared to wildtype PK15 cells (>24 hpi) and supernatant (>48hpi)(P < 0.05). Identification of a non-conservative substitution in this key domain of SYNGR2 suggests that the SYNGR2 p.Arg63Cys variant may underlie the observed genetic effect on viral load.
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Affiliation(s)
- Lianna R. Walker
- Animal Science Department, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Taylor B. Engle
- Animal Science Department, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Hiep Vu
- Animal Science Department, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Emily R. Tosky
- Animal Science Department, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Dan J. Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Timothy P. L. Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Tudor Borza
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Canada
| | - Thomas E. Burkey
- Animal Science Department, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Graham S. Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Stephen D. Kachman
- Department of Statistics, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Daniel C. Ciobanu
- Animal Science Department, University of Nebraska, Lincoln, Nebraska, United States of America
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Kreikemeier CA, Engle TB, Lucot KL, Kachman SD, Burkey TE, Ciobanu DC. Genome-wide analysis of TNF-alpha response in pigs challenged with porcine circovirus 2b. Anim Genet 2015; 46:205-8. [PMID: 25643812 DOI: 10.1111/age.12262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2014] [Indexed: 11/30/2022]
Abstract
Tumor necrosis factor alpha (TNF-α) is a pro-inflammatory cytokine with a role in activating adaptive immunity to viral infections. By inhibiting the capacity of plasmacytoid dendritic cells to produce interferon-α and TNF-α, porcine circovirus 2 (PCV2) limits the maturation of myeloid dendritic cells and impairs their ability to recognize viral and bacterial antigens. Previously, we reported QTL for viremia and immune response in PCV2-infected pigs. In this study, we analyzed phenotypic and genetic relationships between TNF-α protein levels, a potential indicator of predisposition to PCV2 co-infection, and PCV2 susceptibility. Following experimental challenge with PCV2b, TNF-α reached the peak at 21 days post-infection (dpi), at which time a difference was observed between pigs that expressed extreme variation in viremia and growth (P < 0.10). A genome-wide association study (n = 297) revealed that genotypes of 56,433 SNPs explained 73.9% of the variation in TNF-α at 21 dpi. Major SNPs were identified on SSC8, SSC10 and SSC14. Haplotypes based on SNPs from a SSC8 (9 Mb) 1-Mb window were associated with variation in TNF-α (P < 0.02), IgG (P = 0.05) and IgM (P < 0.13) levels at 21 dpi. Potential overlap of regulatory mechanisms was supported by the correlations between genomic prediction values of TNF-α and PCV2 antibodies (21 dpi, r > 0.22), viremia (14-21 dpi, P > 0.29) and viral load (r = 0.31, P < 0.0001). Characterization of the QTL regions uncovered genes that could influence variation in TNF-α levels as well as T- and B-cell development, which can affect disease susceptibility.
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Affiliation(s)
- C A Kreikemeier
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583, USA
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Engle TB, Jobman EE, Moural TW, McKnite AM, Bundy JW, Barnes SY, Davis EH, Galeota JA, Burkey TE, Plastow GS, Kachman SD, Ciobanu DC. Variation in time and magnitude of immune response and viremia in experimental challenges with Porcine circovirus 2b. BMC Vet Res 2014; 10:286. [PMID: 25472653 PMCID: PMC4264338 DOI: 10.1186/s12917-014-0286-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/19/2014] [Indexed: 12/01/2022] Open
Abstract
Background Porcine circovirus 2 is the primary agent responsible for inducing a group of associated diseases known as Porcine Circovirus Associated Diseases (PCVAD), which can have detrimental effects on production efficiency as well as causing significant mortality. The objective of this study was to evaluate variation in viral replication, immune response and growth across pigs (n = 974) from different crossbred lines. The approach used in this study was experimental infection with a PCV2b strain of pigs at an average of 43 days of age. Results The sequence of the PCV2b isolate used in the challenge was similar with a cluster of PCV2b isolates known to induce PCVAD and increased mortality rates. The swine leukocyte antigen class II (SLAII) profile of the population was diverse, with nine DQB1 haplotypes being present. Individual viremia and antibody profiles during challenge demonstrate variation in magnitude and time of viral surge and immune response. The correlations between PCV2 specific antibodies and average daily gain (ADG) were relatively low and varied between - 0.14 to 0.08 for IgM and −0.02 and 0.11 for IgG. In contrast, PCV2 viremia was an important driver of ADG decline following infection; a moderate negative correlation was observed between viral load and overall ADG (r = − 0.35, P < 0.001). The pigs with the lowest 10% level of viral load maintained a steady increase in weekly ADG (P < 0.0001) compared to the pigs that had the 10% greatest viral load (P < 0.55). In addition, the highly viremic group expressed higher IgM and IgG starting with d 14 and d 21 respectively, and higher tumor necrosis factor – alpha (TNF-α) at d 21 (P < 0.005), compared to low viremic group. Conclusions Molecular sources of the observed differences in viremia and immune response could provide a better understanding of the host factors that influence the development of PCVAD and lead to improved knowledge of swine immunity. Electronic supplementary material The online version of this article (doi:10.1186/s12917-014-0286-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taylor B Engle
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Erin E Jobman
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Timothy W Moural
- School of Veterinary Medicine and Biological Sciences, University of Nebraska, Lincoln, USA. .,Bluegrass Community & Technical College, Lexington, USA.
| | - Autumn M McKnite
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Justin W Bundy
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Sarah Y Barnes
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Emily H Davis
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Judith A Galeota
- School of Veterinary Medicine and Biological Sciences, University of Nebraska, Lincoln, USA.
| | - Thomas E Burkey
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
| | | | - Daniel C Ciobanu
- Animal Science Department, University of Nebraska, Lincoln, NE, 68583-0908, USA.
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