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 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.

Decline of genetic variability in a captive population of Pacific white shrimp Penaeus (Litopenaeus) vannamei using microsatellite and pedigree information

Background: The objective of this study was to estimate the decline of genetic variability and the changes in effective population size in three shrimp populations. One was a wild population collected at several points in the Mexican Pacific Ocean. The other two populations were different generations (7 and 9) from a captive population selected for growth and survival. Microsatellite markers and pedigree were both used to assess genetic variability and effective population size. Results: Using 26 loci, both captive populations showed a decline in the expected heterozygosity (20%) and allelic diversity indices (48 to 91%) compared to the wild population (P < 0.05). The studied captive populations did not differ significantly from each other regarding their expected heterozygosity or allelic diversity indices (P > 0.05). Effective population size estimates based on microsatellites declined from 48.2 to 64.0% in cultured populations (P < 0.05) compared to the wild population. Conclusions: An important decline of genetic variability in the cultured selected population due to domestication, and evidence of a further smaller decline in effective population size across generations in the selected population were observed when analyzing pedigree (41%) and microsatellite data (37%). Pedigree keeping is required to prevent the decline of effective population size and maintain genetic variability in shrimp breeding programs, while microsatellites are useful to assess effective population size changes at the population level.