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Published on: December 3, 2011
Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported
José Francisco Rivera-Benítez1, Rebeca Martínez-Bautista2, Raúl González-Martínez3
1Posgrado en Ciencias de la Producción y de la Salud Animal, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
Abstract:
The characteristics of the whole PEDV genome that has circulated in Mexico from the first outbreak to the present are unknown. We chose samples obtained from 2013 to 2017 and sequenced them, which enabled us to identify the genetic variation and phylogeny in the virus during the first four years that it circulated in Mexico. A 99% identity was found among the analyzed pandemic strains; however, the 1% difference affected the structure of the S glycoprotein, which is essential for the binding of the virus to the cellular receptor. The S protein induces the most efficacious antibodies; hence, these changes in structure could be implicated in the clinical antecedents of the outbreaks. Antigenic changes could also help PEDV avoid neutralization, even in the presence of previous immunity. The characterization of the complete genome enabled the identification of three circulating strains that have a deletion in ORF1a, which is present in attenuated Asian vaccine strains. The phylogenetic analysis of the complete genome indicates that the first PEDV outbreaks in Mexico were caused by INDEL strains and pandemic strains related to USA strains; however, the possibility of the entry of European strains exists, which may have caused the 2015 and 2016 outbreaks.
Insights
The genetic makeup of Porcine Epidemic Diarrhea Virus (PEDV) in Mexico was analyzed from 2013-2017. Minor genomic changes, particularly in the S protein, may influence viral evolution and immune evasion.
Area of Science:
- Veterinary Virology
- Molecular Epidemiology
- Genomics
Background:
- The genetic diversity and evolutionary trajectory of Porcine Epidemic Diarrhea Virus (PEDV) in Mexico remain largely uncharacterized.
- Understanding PEDV genome evolution is crucial for disease control and vaccine development.
Purpose of the Study:
- To investigate the genetic variation and phylogenetic relationships of PEDV strains circulating in Mexico between 2013 and 2017.
- To identify key genetic markers associated with PEDV outbreaks in the region.
Main Methods:
- Whole-genome sequencing of PEDV samples collected from 2013 to 2017.
- Phylogenetic analysis to determine the evolutionary history and origins of Mexican PEDV strains.
- Comparative genomic analysis to identify genetic variations, including deletions and mutations.
Main Results:
- High overall genomic identity (99%) among Mexican PEDV strains, with significant variations in the S glycoprotein structure.
- Identification of three circulating strains with deletions in ORF1a, a feature shared with attenuated Asian vaccine strains.
- Phylogenetic analysis suggests initial outbreaks were caused by INDEL and USA-related pandemic strains, with potential European strain introduction impacting later outbreaks.
Conclusions:
- The observed 1% genomic difference, particularly in the S protein, may contribute to PEDV's ability to evade host immunity and influence outbreak clinical characteristics.
- The presence of ORF1a deletions in Mexican strains warrants further investigation regarding their impact on virulence and vaccine efficacy.
- Understanding the complex origins and evolution of PEDV in Mexico is vital for implementing effective biosecurity and control strategies.
