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Genetic Variant Detection in the CALR gene using High Resolution Melting Analysis
Published on: August 26, 2020
Application of high-resolution melting-curve analysis on pvpA gene for detection and classification of Mycoplasma
Shabnam Hashemi1, Mohammadreza Mahzounieh1, Nariman Sheikhi2
1Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.
Abstract:
Mycoplasma gallisepticum (MG) is an avian species pathogen which causes heavy economic losses in the poultry industry. The purpose of this study was to determine genomic diversity of 14 MG field strains from chicken, Chuker partridge and peacock collected during 2009-2012 in Iran by polymerase chain reaction and partial sequencing of the pvpA gene. A High-Resolution Melting (HRM) technique was also developed and applied to differentiate between field and vaccine strains. Sequencing of the pvpA gene revealed a 51 nucleotide deletion, within DR-1 and DR-2, among MG strains from chicken and partridge whilst 63 nucleotides were deleted in MG strain from peacock. One nucleotide substitution was also observed among chicken MG strains. Phylogenetic analysis of the sequences clustered all of the Iranian MG strains into two clades or phylogeny groups; the strains from chicken and partridge in one group (group 1) and the strain from peacock into another group (group 4). HRM analysis has also produced comparable outcome to those of sequencing; four distinct melting curves which correspond to the three MG strains from chicken, Chukar partridge and peacock and ts-11 vaccine strain. Overall, findings of this study point towards a single source of infection for the chicken and partridge MG strains and likelihood of the strains being native and endemic in Iran. Peacock considered as an exotic species in Iran, hence the genetic distance for the pvpA gene. MG can be transmitted easily among different avian species and this distinct peacock strain may pose a threat to poultry industry. Our findings also show that molecular variation among pvpA gene of MG strains could be revealed using the relatively rapid and affordable HRM technique.
Insights
Genomic diversity of Mycoplasma gallisepticum (MG) in Iran was analyzed using pvpA gene sequencing and HRM. Findings suggest endemic chicken and partridge strains, with a distinct peacock strain posing a potential poultry industry threat.
Area of Science:
- Avian Pathogen Genomics
- Molecular Epidemiology
- Poultry Health
Background:
- Mycoplasma gallisepticum (MG) causes significant economic losses in the poultry industry.
- Understanding MG genomic diversity is crucial for disease control and prevention.
- Previous studies have not fully characterized Iranian MG field strains.
Purpose of the Study:
- To determine the genomic diversity of 14 Mycoplasma gallisepticum field strains from Iran.
- To differentiate between field and vaccine strains using High-Resolution Melting (HRM) analysis.
- To investigate the evolutionary relationships and potential origins of Iranian MG strains.
Main Methods:
- Polymerase chain reaction (PCR) and partial sequencing of the pvpA gene.
- Development and application of High-Resolution Melting (HRM) technique.
- Phylogenetic analysis of pvpA gene sequences.
Main Results:
- Sequencing revealed nucleotide deletions and substitutions in the pvpA gene among different avian hosts.
- Phylogenetic analysis clustered Iranian MG strains into two distinct groups.
- HRM analysis successfully differentiated field strains from the vaccine strain, correlating with sequencing data.
Conclusions:
- Chicken and partridge MG strains likely share a common, endemic source in Iran.
- A distinct peacock MG strain, potentially exotic, may pose a threat to poultry.
- The HRM technique is a rapid and affordable method for revealing molecular variations in MG pvpA genes.
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