Porcine deltacoronavirus has caused great economic losses in the swine industry worldwide. In this study, we carried out the first detection, sequencing and characterization of this virus in Mexico. We analysed 885 rectal samples by multiplex RT‐PCR to determine coinfections. In addition, the Spike gene was amplified, sequenced and analysed phylogenetically. We found 85 positive samples for porcine deltacoronavirus, representing 9.6% of the total samples, and we determined that the most frequent coinfection was with porcine epidemic diarrhoea virus (54.1%). Four sequences of Mexican isolates were most closely related to those of the United States. The antigenic regions and the glycosylation site of the strains obtained coincide with those previously reported. This relationship is probably related to the commercial exchange of pigs between the US and Mexico and the geographical proximity of these two countries.

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.

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We sampled sera from 1013 non-vaccinated swine from four states in Mexico, Guanajuato, Jalisco, Michoacán and the Estado de Mexico, to analyse anti-porcine rubulavirus antibody titres against three different porcine rubulavirus isolates (PAC-4/1993, PAC-6/2001, and PAC-9/2003) using a hemagglutination inhibition assay. The results revealed that there were antigenic differences among the isolates assessed. In particular, the estimated correlation between the PAC-4/1993 and PAC-6/2001 (0.50) isolates and between the PAC-4/1993 and PAC-9/2003 isolates (0.56) displayed a moderate positive correlation. In contrast, there was a strong positive correlation between the PAC-6/2001 and PAC-9/2003 isolates (0.73). We also found that in the state of Guanajuato, PAC-4/1993 was the isolate that was most frequently identified; in Jalisco, the isolate was PAC-6/2001; and in Michoacán, the isolate was PAC-9/2003. By contrast, in the Estado de Mexico, all three isolates appeared to circulate with a low seroprevalence. In general, the analysed sera from the four states displayed a porcine rubulavirus serological prevalence ranging from 9% to 23.7%. These data indicate that there is not complete antibody cross-antigenicity among the three isolates, and the antigenic variations in the antibody response found in this study implies that the use of a monovalent vaccine would not generate complete protection against the different antigenic subtypes.

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