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Buter R, Feberwee A, de Wit S, Heuvelink A, da Silva A, Gallardo R, Soriano Vargas E, Swanepoel S, Jung A, Tödte M, Dijkman R. Molecular characterization of the HMTp210 gene of Avibacterium paragallinarum and the proposition of a new genotyping method as alternative for classical serotyping. Avian Pathol 2023; 52:362-376. [PMID: 37470411 DOI: 10.1080/03079457.2023.2239178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
Avibacterium paragallinarum (A. paragallinarum) is the aetiological agent of infectious coryza (IC) in chickens and characterized by acute respiratory distress and severe drop in egg production. Vaccination is important in the control of IC outbreaks and the efficacy of vaccination is dependent on A. paragallinarum serovars included in the vaccine. Classical serotyping of A. paragallinarum is laborious and hampered by poor availability of antigens and antisera. The haemagglutinin, important in classical serotyping, is encoded by the HMTp210 gene. HMTp210 gene analysis has been shown to have potential as alternative to classical serotyping. The aim of the present study was to further investigate the potential of sequence analyses of partial region 1 of the HMTp210 gene, the HMTp210 hypervariable region and the concatenated sequences of both fragments. For this analysis, 123 HMTp210 gene sequences (field isolates, A. paragallinarum serovar reference strains and vaccine strains) were included. Evaluation of serovar references and vaccine strains revealed a need for critical evaluation, especially within Page serovar B and C. Phylogenetic analysis of HMTp210 region 1 resulted in a separation of Page serovar A, B and C strains. Analysis of the HMTp210 HVR alone was not sufficient to discriminate all nine different Kume serovar references. The concatenated sequences of HMTp210 region 1 and HMTp210 HVR resulted in 14 clusters with a high correlation with Page serovar and with the nine currently known Kume serovars and is therefore proposed as a novel genotyping method that could be used as an alternative for classical serotyping of A. paragallinarum.
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Affiliation(s)
| | | | - Sjaak de Wit
- Royal GD, Deventer, the Netherlands
- Department of Population Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | - Ana da Silva
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Rodrigo Gallardo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Edgardo Soriano Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Toluca, México
| | - Stefan Swanepoel
- Deltamune, Unit 34, Oxford Business Park, Centurion, South Africa
| | - Arne Jung
- Klinik für Geflügel, University of Veterinary Medicine, Hannover, Germany
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Bien SA, Pankow JS, Haessler J, Lu Y, Pankratz N, Rohde RR, Tamuno A, Carlson CS, Schumacher FR, Bůžková P, Daviglus ML, Lim U, Fornage M, Fernandez-Rhodes L, Avilés-Santa L, Buyske S, Gross MD, Graff M, Isasi CR, Kuller LH, Manson JE, Matise TC, Prentice RL, Wilkens LR, Yoneyama S, Loos RJF, Hindorff LA, Le Marchand L, North KE, Haiman CA, Peters U, Kooperberg C. Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology ( PAGE) consortium. Diabetologia 2017; 60:2384-2398. [PMID: 28905132 PMCID: PMC5918310 DOI: 10.1007/s00125-017-4405-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 07/06/2017] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Elevated levels of fasting glucose and fasting insulin in non-diabetic individuals are markers of dysregulation of glucose metabolism and are strong risk factors for type 2 diabetes. Genome-wide association studies have discovered over 50 SNPs associated with these traits. Most of these loci were discovered in European populations and have not been tested in a well-powered multi-ethnic study. We hypothesised that a large, ancestrally diverse, fine-mapping genetic study of glycaemic traits would identify novel and population-specific associations that were previously undetectable by European-centric studies. METHODS A multiethnic study of up to 26,760 unrelated individuals without diabetes, of predominantly Hispanic/Latino and African ancestries, were genotyped using the Metabochip. Transethnic meta-analysis of racial/ethnic-specific linear regression analyses were performed for fasting glucose and fasting insulin. We attempted to replicate 39 fasting glucose and 17 fasting insulin loci. Genetic fine-mapping was performed through sequential conditional analyses in 15 regions that included both the initially reported SNP association(s) and denser coverage of SNP markers. In addition, Metabochip-wide analyses were performed to discover novel fasting glucose and fasting insulin loci. The most significant SNP associations were further examined using bioinformatic functional annotation. RESULTS Previously reported SNP associations were significantly replicated (p ≤ 0.05) in 31/39 fasting glucose loci and 14/17 fasting insulin loci. Eleven glycaemic trait loci were refined to a smaller list of potentially causal variants through transethnic meta-analysis. Stepwise conditional analysis identified two loci with independent secondary signals (G6PC2-rs477224 and GCK-rs2908290), which had not previously been reported. Population-specific conditional analyses identified an independent signal in G6PC2 tagged by the rare variant rs77719485 in African ancestry. Further Metabochip-wide analysis uncovered one novel fasting insulin locus at SLC17A2-rs75862513. CONCLUSIONS/INTERPRETATION These findings suggest that while glycaemic trait loci often have generalisable effects across the studied populations, transethnic genetic studies help to prioritise likely functional SNPs, identify novel associations that may be population-specific and in turn have the potential to influence screening efforts or therapeutic discoveries. DATA AVAILABILITY The summary statistics from each of the ancestry-specific and transethnic (combined ancestry) results can be found under the PAGE study on dbGaP here: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000356.v1.p1.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA.
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Yinchang Lu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Rebecca R Rohde
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alfred Tamuno
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Martha L Daviglus
- Department of Medicine, Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Myriam Fornage
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lindsay Fernandez-Rhodes
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Larissa Avilés-Santa
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Newark, NJ, USA
| | - Myron D Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Mariaelisa Graff
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carmen R Isasi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lewis H Kuller
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Ross L Prentice
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Sachiko Yoneyama
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Ruth J F Loos
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lucia A Hindorff
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
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