Abstract
Porcine enteric coronaviruses include some of the most relevant viral pathogens to the swine industry such as porcine epidemic diarrhea virus (PEDV) or porcine transmissible gastroenteritis virus (TGEV) as well as several recently identified virus such as swine enteric coronavirus (SeCoV), porcine deltacoronavirus (PDCoV) or swine enteric alphacoronavirus (SeACoV). The aim of this study is the identification and characterization of enteric coronaviruses on Spanish pig farms between 2017 and 2019. The study was carried out on 106 swine farms with diarrhea outbreaks where a viral etiology was suspected by using two duplex RT-PCRs developed for the detection of porcine enteric coronaviruses. PEDV was the only coronavirus detected in our research (38.7% positive outbreaks, 41 out of 106) and neither TGEV, SeCoV, PDCoV nor SeACoV were detected in any of the samples. The complete S-gene of all the PEDV isolates recovered were obtained and compared to PEDV and SeCoV sequences available in GenBank. The phylogenetic tree showed that only PEDV of the INDEL 2 or G1b genogroup has circulated in Spain between 2017 and 2019. Three different variants were detected, the recombinant PEDV-SeCoV being the most widespread. These results show that PEDV is a relevant cause of enteric disorders in pigs in Spain while new emerging coronavirus have not been detected so far. However, the monitoring of these virus is advisable to curtail their emergence and spread.
Highlights
Coronaviruses (CoVs) are found in a wide variety of animals including both mammals and birds in which they cause a variety of respiratory, enteric or even hepatic and neurological disorders [1]
porcine epidemic diarrhea virus (PEDV) was involved to a lesser extent in diarrhea outbreaks affecting nursing piglets, no significant differences in the number of PEDV confirmed outbreaks between age groups arose when compared using the Fisher exact test (p = 0.094)
A hundred and six viral suspected diarrhea outbreaks were investigated between 2017 and 2019 and confirmed that PEDV was the only enteric coronavirus detected in swine farms in Spain
Summary
Coronaviruses (CoVs) are found in a wide variety of animals including both mammals and birds in which they cause a variety of respiratory, enteric or even hepatic and neurological disorders [1]. They belong to the Coronaviridae family which recognizes four genera based on phylogenetic clustering: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. From the 5′ end to the 3′ end, their genomic structure is made up of at least six open reading frames (ORFs) named ORF1a, ORF1b, spike (S), envelope (E), membrane (M), and nucleocapsid (N). Two species of the Alphacoronavirus genus, transmissible gastroenteritis virus (TGEV) and the porcine epidemic diarrhea virus (PEDV) have long been recognized as the cause of acute diarrhea outbreaks on swine farms affecting pigs of all ages and causing high mortality in lactating piglets
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