Molecular Detection and Characterization of Porcine Epidemic Diarrhea Virus and Porcine Aichivirus C Coinfection in México

Montserrat-Elemi García-Hernández,Blanca Itzel Taboada-Ramírez,Sofía-Lizbeth Alcaraz-Estrada,Rosa-Elena Sarmiento-Silva,María-Elena Trujillo-Ortega,Carlos Sandoval-Jaime,Luis Lozano-Aguirre-Beltrán

doi:10.3390/v13050738

Montserrat-Elemi García-Hernández, Blanca Itzel Taboada-Ramírez + Show 5 more

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https://doi.org/10.3390/v13050738

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Abstract

Swine enteric viral infections are responsible for substantial economic losses in the pork industry worldwide. Porcine epidemic diarrhea (PEDV) is one of the main causative agents of diarrhea in lactating pigs, and reports of PEDV coinfection with other enteric viruses highlight the importance of viral interactions for disease presentation and outcomes. Using next-generation sequencing (NGS) and sequence analyses from samples taken from piglets with acute diarrhea, we explored the possible interactions between PEDV and other less reported pathogens. PEDV coinfection with porcine kobuvirus (PKV) was detected in 36.4% (27/74) of samples. Full genomes from porcine coronavirus and kobuvirus were obtained, as was a partial porcine sapovirus genome (PSaV). The phylogenetic results show the clustering of these strains corresponding to the geographical relationship. To our knowledge, this is the first full genome and isolation report for porcine kobuvirus in México, as well as the first phylogenetic analysis for porcine sapovirus in the country. The NGS approach provides a better perspective of circulating viruses and other pathogens in affected production units.

Highlights

Diarrheic diseases in swine have strong economic impacts on production units around the world
We explored next-generation sequencing (NGS) as a tool for the identification of viral pathogens during an outbreak of diarrhea in a commercial farm, making the detection and characterization of natural viral coinfection in diarrheic piglets possible
Coinfection of porcine kobuvirus (PKV) and Porcine epidemic diarrhea virus (PEDV) was detected in 80% (8/10) of the analyzed farms located in Nuevo León, Guanajuato, and Estado de México states

Summary

Introduction

Diarrheic diseases in swine have strong economic impacts on production units around the world. Porcine epidemic diarrhea virus (PEDV) induces an enteric disease with high mortality rates in suckling piglets characterized by acute diarrhea and severe dehydration. It was first identified in Europe in 1978 and in Asia in 1982. PEDV has had a great impact on the Asian swine industry. In May 2013, the presence of PEDV was reported in México along with the United States and Canada, resulting in heavy economic losses for the swine production units [3,4]

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