Molecular characterization of the spike gene of the porcine epidemic diarrhea virus in Mexico, 2013–2016

Abstract

In Mexico, the first outbreaks suggestive of the circulation of the porcine epidemic diarrhea virus (PEDV) were identified at the beginning of July 2013. To identify the molecular characteristics of the PEDV Spike (S) gene in Mexico, 116 samples of the intestine and diarrhea of piglets with clinical signs of porcine epidemic diarrhea (PED) were obtained. Samples were collected from 14 farms located in six states of Mexico (Jalisco, Puebla, Sonora, Veracruz, Guanajuato, and Michoacán) from 2013 to 2016. To identify PEDV, we used real-time RT-PCR to discriminate between non-INDEL and INDEL strains. We chose samples according to state and year to characterize the S gene. After amplification of the S gene, the obtained products were sequenced and assembled. The complete amino acid sequences of the spike protein were used to perform an epitope analysis, which was used to determine null mutations in regions SS2, SS6, and 2C10 compared to the sequences of G2. A phylogenetic analysis determined the circulation of G2b and INDEL strains in Mexico. However, several mutations were recorded in the collagenase equivalent (COE) region that were related to the change in polarity and charge of the amino acid residues. The PEDV strain circulating in Jalisco in 2016 has an insertion of three amino acids (LGL) and one change in the antigenic site of the COE region, and strains from the years 2015 and 2016 changed the index of the surface probability, which could be related to the re-emergence of disease outbreaks.

Emerging strains of porcine epidemic diarrhoea virus (PEDv) in Mexico

“…The PEDv S gene was amplified by endpoint RT‐PCR, yielding 28 positive samples (52.83%) from 10 of the 17 states sampled. This study reports the presence of the PEDv S gene in the states of Hidalgo, Oaxaca and San Luis Potosí for the first time (Lara‐Romero et al, ; OIE, ). The coronavirus S protein is a type I membrane glycoprotein that interacts with cell receptors during virus entry (Weiss & Leibowitz, ).…”

“…Various genotypes of the S protein gene have been described based on their genetic traits and the period when the strains emerged: GIa (classical), GIb (emergent, Indel‐S), GIIa (emergent, non‐Indel‐S from the Americas) and GIIb (emergent, non‐Indel‐S from Asia) (Jarvis et al, ; Lee, ). Previous studies in Mexico have identified circulating strains with a GII genotype (from the Americas) as well as strains with a GI genotype (Indel‐S) (Lara‐Romero et al, ). The 20 strains isolated in this study (Table ) are in the GIIa genotype branch and were identified as emerging, non‐Indel‐S variants (Figure ); the strains PEDv/MEX/JAL/LI‐DMZC11/2015 and PEDv/MEX/MICH/LI‐DMZC19/2015 are located in a cluster related to emerging strains from Asia, and all other strains are in clusters along with strains from the Americas (Jarvis et al, ; Lee, ), indicating that a wide range of strains are circulating in Mexico.…”

“…The 2‐amino acid insertion 537 SQ 538 was identified herein in the COE region in the strain PEDv/MEX/QRO/LI‐DMZC49/2016; this insertion could give the S protein a different biological activity. Recently, 11 substitutions were found in 7 different Mexican strains (Lara‐Romero et al, ); one of these substitutions (H 524 R) was found in a strain from Sonora. In this work, amino acid substitutions were found in strains from Puebla, Veracruz and Querétaro.…”

“…Indel‐S‐type strains have been found in several countries where the disease is endemic; however, they have been described as highly pathogenic strains (Stadler et al, ). The circulation of Indel‐S and non‐Indel‐S strains was recently described in Mexico, reporting PEDv prevalence levels of 30% (OIE, ) and 88.8% (Lara‐Romero et al, ). Previous reports on porcine epidemic diarrhoea in other countries suggest that the high genetic diversity of the circulating strains could produce emerging strains not yet identified in Mexico.…”

Biological characterization and pathogenicity of a newly isolated Chinese highly virulent genotype GIIa porcine epidemic diarrhea virus strain

“…PEDV variants emerged in the United States starting in May 2013 and then spread rapidly throughout the nation. Many American, Asian and European countries, including Canada, Mexico, Colombia, Japan, South Korea, the Philippines, Thailand, Germany, the Netherlands and Switzerland have also reported outbreaks of PED [6,[8][9][10][11][12][13].…”