Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017)
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 tha...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-02-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/16/2/309 |
| _version_ | 1797296806571278336 |
|---|---|
| author | José Francisco Rivera-Benítez Rebeca Martínez-Bautista Raúl González-Martínez Jazmín De la Luz-Armendáriz Irma Herrera-Camacho Nora Rosas-Murrieta Laura Márquez-Valdelamar Rocio Lara |
| author_facet | José Francisco Rivera-Benítez Rebeca Martínez-Bautista Raúl González-Martínez Jazmín De la Luz-Armendáriz Irma Herrera-Camacho Nora Rosas-Murrieta Laura Márquez-Valdelamar Rocio Lara |
| author_sort | José Francisco Rivera-Benítez |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-07T22:10:09Z |
| format | Article |
| id | doaj.art-6a294e61783e46a99d21320ca51ed5c8 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-07T22:10:09Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6a294e61783e46a99d21320ca51ed5c82024-02-23T15:37:46ZengMDPI AGViruses1999-49152024-02-0116230910.3390/v16020309Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017)José Francisco Rivera-Benítez0Rebeca Martínez-Bautista1Raúl González-Martínez2Jazmín De la Luz-Armendáriz3Irma Herrera-Camacho4Nora Rosas-Murrieta5Laura Márquez-Valdelamar6Rocio Lara7Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Mexico City 04010, MexicoZoetis Swine, Mexico City 05120, MexicoCargill, Mexico City 01210, MexicoDepartamento de Medicina y Zootecnia de Rumiantes, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, MexicoLaboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72000, MexicoLaboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72000, MexicoLaboratorio de Secuenciación Genómica de la Biodiversidad y de la Salud, UNAM, Mexico City 04510, MexicoPrograma de Maestría en Ciencias de la Producción y de la Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, MexicoThe 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.https://www.mdpi.com/1999-4915/16/2/309porcine epidemic diarrhea virusphylogenetic analysisspike protein |
| spellingShingle | José Francisco Rivera-Benítez Rebeca Martínez-Bautista Raúl González-Martínez Jazmín De la Luz-Armendáriz Irma Herrera-Camacho Nora Rosas-Murrieta Laura Márquez-Valdelamar Rocio Lara Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017) Viruses porcine epidemic diarrhea virus phylogenetic analysis spike protein |
| title | Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017) |
| title_full | Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017) |
| title_fullStr | Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017) |
| title_full_unstemmed | Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017) |
| title_short | Phylogenetic and Molecular Analysis of the Porcine Epidemic Diarrhea Virus in Mexico during the First Reported Outbreaks (2013–2017) |
| title_sort | phylogenetic and molecular analysis of the porcine epidemic diarrhea virus in mexico during the first reported outbreaks 2013 2017 |
| topic | porcine epidemic diarrhea virus phylogenetic analysis spike protein |
| url | https://www.mdpi.com/1999-4915/16/2/309 |
| work_keys_str_mv | AT josefranciscoriverabenitez phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT rebecamartinezbautista phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT raulgonzalezmartinez phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT jazmindelaluzarmendariz phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT irmaherreracamacho phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT norarosasmurrieta phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT lauramarquezvaldelamar phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 AT rociolara phylogeneticandmolecularanalysisoftheporcineepidemicdiarrheavirusinmexicoduringthefirstreportedoutbreaks20132017 |