during 20072014 , we collected 27 fecal and 24 intestinal samples from pigs with suspected pedv or tgev infections ; the pigs came from swine farms in northern italy ( po valley ) , which contains the regions of piemonte , lombardia , emilia romagna , and veneto ( technical appendix figure 1 ) . clinical signs included watery diarrhea in sows and a death rate in piglets of 5%10% , lower than is typical with pedv or tgev infections . samples were submitted for testing by electron microscopy , pedv elisa , viral isolation , pan - cov reverse transcription pcr ( rt - pcr ) , and rt - pcr for prcv and tgev ; selected positive pan - cov samples were sequenced ( 1214 ) ( technical appendix ) . results of electron microscopy showed that 25 ( 49% ) of the 51 samples contained cov - like particles , but all samples were negative for viral isolation . although only 38 samples ( 74% ) were positive by pan - cov rt - pcr , 47 ( 92% ) were positive by the pedv elisa ( table 1 ) ( 12,13 ) . of the 38 pan - cov  positive samples , 18 were selected for partial rna - dependent rna polymerase ( rdrp ) , spike ( s1 ) ( 14 ) , and membrane ( m ) sequencing ( table 1 ) . all samples were negative for prcv and tgev by rt - pcr , ruling out co - infection with pedv and tgev or prcv ( 15 ) . * cluster i represents strains circulating from 2007 through mid-2009 ; cluster ii represents strains circulating from mid-2009 through 2012 ; and cluster iii represents strains circulating since 2014 . em , electron microscopy ; m , membrane ; pan - cov rt - pcr , pan - coronavirus reverse transcription pcr ; pedv , porcine epidemic diarrhea virus ; prcv , porcine respiratory coronavirus ; rdrp , rna - dependent rna polymerase ; s1 , spike ; tgev , transmissible gastroenteritis virus ; + , positive ;  , negative ; na , not tested or sequenced . samples selected for whole genome sequencing .   on the basis of the partial sequences from rdrp and the s1 and m genes , the strains from italy clustered into 3 temporally divided groups , suggesting 3 independent virus entries . cluster i represents strains circulating from 2007 through mid-2009 ; cluster ii represents strains circulating from mid-2009 through 2012 ; and cluster iii represents strains circulating since 2014 ( technical appendix figure 2 , panels a  c ) . cluster i was identified in emilia romagna ( n = 1 ) , lombardia ( n = 5 ) , and veneto ( n = 1 ) . cluster ii was identified in emilia romagna ( n = 1 ) and lombardia ( n = 8) . cluster iii was identified in emilia romagna at 2 swine farms . to help explain the temporal clustering , a single s1 gene segment was sequenced from clusters i and ii ( pedv / italy/7239/2009 and secov / italy/213306/2009 , respectively ) . because of the recent outbreak of pedv in europe , the 2 positive samples from cluster iii ( pedv / italy/178509/2014 and pedv / italy/200885/2014 ) were sequenced ( figure 1 , panel a ) . a ) analysis performed on the basis of the nucleotide sequence of the complete spike ( s1 ) gene of 4 representative strains from the 3 clusters and b ) whole genome of 2 positive strains from clusters i and ii . cluster i represents strains circulating from 2007 through mid-2009 ; cluster ii represents strains circulating from mid-2009 through 2012 ; and cluster iii represents strains circulating since 2014 . the strains from this study are represented in blue ; strains from china are green ; strains from north america are red ; and strains from europe are purple . pedv , porcine epidemic diarrhea virus ; prcv , porcine respiratory coronavirus ; tgev , transmissible gastroenteritis virus ; secov , swine enteric coronavirus . one strain from each cluster was selected for whole genome sequencing ( technical appendix ) . unfortunately , the whole genome was obtained from only clusters i and ii ( pedv / italy/7239/2009 and secov / italy/213306/2009 , respectively ; figure 1 , panel b ) . recombination analysis was conducted on the 2 whole genomes and was not detected in pedv / italy/7239/2009 . recombination was detected in secov / italy/213306/2009 at position 20636 and 24867 of pedv cv777 and at position 20366 and 24996 of tgev h16 ( figure 2 ) , suggesting the occurrence of a recombination event between a pedv and a tgev . the complete s gene of secov / italy/213306/2009 shared 92% and 90% nt identity with the prototype european strain pedv cv777 and the original highly virulent north american strain colorado 2013 , respectively , and the remaining genome shared a 97% nt identity with the virulent strains tgev h16 and tgev miller m6 . whole - genome analysis of pedv / italy/7239/2009 showed that it grouped with the global pedv strains ( 6 ) and shared 97% nt identity with pedv strains cv777 , dr13 virulent , and north american s - indel strain oh851 ( table 2 ) . potential recombination points in the secov strains in study of swine enteric coronaviruses in italy . the potential parent strains h16 ( tgev ) and cv777 ( pedv ) are shown in teal and purple , respectively . pedv , porcine epidemic diarrhea virus ; tgev , transmissible gastroenteritis virus ; secov , swine enteric coronavirus . * cluster i represents strains circulating from 2007 through mid-2009 ; cluster ii represents strains circulating from mid-2009 through 2012 . ger , germany ; orf , open reading frame ; prcv , porcine respiratory coronavirus ; pedv , porcine epidemic diarrhea virus ; secov , swine enteric coronavirus ; tgev , transmissible gastroenteritis virus during 20072014 , most ( 92% ) samples collected from the po valley in italy were positive for pedv by elisa ; only 72% were positive by pan - cov pcr . however , because we were investigating the presence of pedv or tgev in samples with clinical signs of diarrhea , the high occurrence of pedv may not reflect the actual prevalence of pedv in italy . the increased percentage of pedv found in samples tested by elisa , compared with the proportion found by pcr , may be explained by the number of ambiguous bases in the pan - cov primers ; the ambiguous bases severely reduce the efficiency of the reaction . the swine enteric cov strains from italy in our study , including the recombinant strain , were reported in pigs with mild clinical signs , indicating that pedv and secov have been circulating in italy and likely throughout europe for multiple years but were underestimated as a mild form of diarrhea .   to understand the evolution of pedv in italy , the partial rdrp , s , and m genes cluster i ( 2007mid 2009 ) resembles the oldest pedv strains ; cluster ii resembles a new tgev and pedv recombinant variant ; and cluster iii , identified from 2 pig farms in northern italy in 2014 , resembles the pedv s - indel strains identified in germany , france , belgium , and the united states . the > 99.3% nt identity of the s1 gene within cluster iii and in previously identified strains could suggest the spread of the s - indel strain into europe . however , directionality of spread can not be determined because of a lack of global and temporal pedv sequences . although our findings could indicate 3 introductions of pedv in italy , the results more likely suggest the high ability of natural recombination among covs and the continued emergence of novel covs with distinct pathogenic properties . further investigation is needed to determine the ancestor of the secov strain or to verify whether the recombinant virus was introduced in italy . recombinant secov was probably generated in a country in which both pedv and tgev are endemic , but because the presence of these viruses in europe is unclear and secov has not been previously described , it is difficult to determine the parental strains and geographic spread of secov . future studies are required to describe the pathogenesis of secov and its prevalence in other countries . technical appendix . additional methods , tables , and figures from study of swine enteric coronaviruses in italy .