Trypsin-independent porcine epidemic diarrhea virus US strain with altered virus entry mechanism.

BACKGROUND: Porcine Epidemic Diarrhea Virus (PEDV) is a coronavirus that infects the intestinal tract and causes diarrhea and vomiting in older pigs or extreme dehydration and death that could reach 100% mortality in neonatal piglets. In the US, the first PEDV outbreaks occurred in 2013 and since then US PEDV strains have quickly spread throughout the US and worldwide, causing significant economic and public health concerns. Currently two conditionally approved vaccines exist in the US, but there is no live attenuated vaccine, which is considered the best option in controlling PEDV by inducing transferrable mucosal immunity to susceptible neonatal piglets. In this study, we passaged an US PEDV isolate under various conditions to generate three strains and characterized their growth and antigenicity in cell culture using various assays including Western blot analysis, serum neutralization assay, sequencing analysis and confocal microscopy. Finally, these strains were evaluated for pathogenicity in nursing piglets (1-4 days old). RESULTS: One of the PEDV strains generated in this study (designated as PEDV 8aa) is able to replicate in cells without any protease and grows to a high titer of >8 log10 TCID50/ml in cell culture. Interestingly, replication of PEDV 8aa was severely reduced by trypsin and this correlated with the inhibition of virus attachment and entry into the cells. In neonatal nursing piglets, PEDV 8aa (passage number 70 or 105) was found to be fully attenuated with limited virus shedding. CONCLUSIONS: These results suggest that applying selective pressure during viral passages can facilitate attainment of viral attenuation and that PEDV 8aa warrants further investigation as an attenuated vaccine.

Pathogenicity and transmissibility of novel reassortant H3N2 influenza viruses with 2009 pandemic H1N1 genes in pigs.

UNLABELLED: At least 10 different genotypes of novel reassortant H3N2 influenza viruses with 2009 pandemic H1N1 [A(H1N1)pdm09] gene(s) have been identified in U.S. pigs, including the H3N2 variant with a single A(H1N1)pdm09 M gene, which has infected more than 300 people. To date, only three genotypes of these viruses have been evaluated in animal models, and the pathogenicity and transmissibility of the other seven genotype viruses remain unknown. Here, we show that three H3N2 reassortant viruses that contain 3 (NP, M, and NS) or 5 (PA, PB2, NP, M, and NS) genes from A(H1N1)pdm09 were pathogenic in pigs, similar to the endemic H3N2 swine virus. However, the reassortant H3N2 virus with 3 A(H1N1)pdm09 genes and a recent human influenza virus N2 gene was transmitted most efficiently among pigs, whereas the reassortant H3N2 virus with 5 A(H1N1)pdm09 genes was transmitted less efficiently than the endemic H3N2 virus. Interestingly, the polymerase complex of reassortant H3N2 virus with 5 A(H1N1)pdm09 genes showed significantly higher polymerase activity than those of endemic and reassortant H3N2 viruses with 3 A(H1N1)pdm09 genes. Further studies showed that an avian-like glycine at position 228 at the hemagglutinin (HA) receptor binding site is responsible for inefficient transmission of the reassortant H3N2 virus with 5 A(H1N1)pdm09 genes. Taken together, our results provide insights into the pathogenicity and transmissibility of novel reassortant H3N2 viruses in pigs and suggest that a mammalian-like serine at position 228 in the HA is critical for the transmissibility of these reassortant H3N2 viruses. IMPORTANCE: Swine influenza is a highly contagious zoonotic disease that threatens animal and public health. Introduction of 2009 pandemic H1N1 virus [A(H1N1)pdm09] into swine herds has resulted in novel reassortant influenza viruses in swine, including H3N2 and H1N2 variants that have caused human infections in the United States. We showed that reassortant H3N2 influenza viruses with 3 or 5 genes from A(H1N1)pdm09 isolated from diseased pigs are pathogenic and transmissible in pigs, but the reassortant H3N2 virus with 5 A(H1N1)pdm09 genes displayed less efficient transmissibility than the endemic and reassortant H3N2 viruses with 3 A(H1N1)pdm09 genes. Further studies revealed that an avian-like glycine at the HA 228 receptor binding site of the reassortant H3N2 virus with 5 A(H1N1)pdm09 genes is responsible for less efficient transmissibility in pigs. Our results provide insights into viral pathogenesis and the transmission of novel reassortant H3N2 viruses that are circulating in U.S. swine herds and warrant future surveillance.

Discovery of a novel nidovirus in cattle with respiratory disease.

The family Coronaviridae represents a diverse group of vertebrate RNA viruses, all with genomes greater than 26,000 nt. Here, we report the discovery and genetic characterization of a novel virus present in cattle with respiratory disease. Phylogenetic characterization of this virus revealed that it clusters within the subfamily Torovirinae, in the family Coronaviridae. The complete genome consists of only 20,261 nt and represents the smallest reported coronavirus genome. We identified seven ORFs, including the canonical nidovirus ORF1a and ORF1b. Analysis of polyprotein 1ab revealed that this virus, tentatively named bovine nidovirus (BoNV), shares the highest homology with the recently described python-borne nidoviruses and contains several conserved nidovirus motifs, but does not encode the NendoU or O-MT domains that are present in other viruses within the family Coronaviridae. In concert with its reduced genome, the atypical domain architecture indicates that this virus represents a unique lineage within the order Nidovirales.

Discovery of a novel putative atypical porcine pestivirus in pigs in the USA.

Pestiviruses are some of the most significant pathogens affecting ruminants and swine. Here, we assembled a 11 276 bp contig encoding a predicted 3635 aa polyprotein from porcine serum with 68 % pairwise identity to that of a recently partially characterized Rhinolophus affinis pestivirus (RaPV) and approximately 25-28 % pairwise identity to those of other pestiviruses. The virus was provisionally named atypical porcine pestivirus (APPV). Metagenomic sequencing of 182 serum samples identified four additional APPV-positive samples. Positive samples originated from five states and ELISAs using recombinant APPV Erns found cross-reactive antibodies in 94 % of a collection of porcine serum samples, suggesting widespread distribution of APPV in the US swine herd. The molecular and serological results suggest that APPV is a novel, highly divergent porcine pestivirus widely distributed in US pigs.

First identification of porcine parvovirus 6 in North America by viral metagenomic sequencing of serum from pigs infected with porcine reproductive and respiratory syndrome virus.

BACKGROUND: Currently, eight species in four genera of parvovirus have been described that infect swine. These include ungulate protoparvovirus 1 (classical porcine parvovirus, PPV), ungulate tetraparvovirus 2 (PPV3), ungulate tetraparvovirus 3 (which includes PPV2, porcine hokovirus, porcine partetravirus and porcine PARV4), ungulate copiparvovirus 2 (which includes PPV4 and PPV5), ungulate bocaparvovirus 2 (which includes porcine bocavirus 1, 2 and 6), ungulate bocaparvovirus 3 (porcine bocavirus 5), ungulate bocaparvovirus 4 (porcine bocavirus 7) and ungulate bocaparvovirus 5 (porcine bocavirus 3, 4-1 and 4-2). PPV6, the most recently described porcine parvovirus, was first identified in China in late 2014 in aborted pig fetuses. Prevalence of PPV6 in China was found to be similar in finishing age pigs from farms with and without evidence of swine reproductive failure. METHODS: Porcine parvovirus 6 (PPV6) was detected by sequence-independent single primer amplification (SISPA) and confirmed by overlapping and real-time PCR in the serum of porcine reproductive and respiratory virus (PRRSv) positive samples. RESULTS: Seven nearly complete genomes of PPV6 were identified in PRRSv genotype 2 positive serum samples submitted to state veterinary diagnostic laboratories in 2014. Further testing using overlapping and real-time PCR determined PPV6 to be present in 13.2 % of the serums tested. Additionally, PPV6 was present in samples from all of the geographic locations sampled encompassing nine states in the United States and one state in Mexico. The presence of PPV6 in serum indicates that the PPV6 infection is disseminated and not localized to a specific tissue type. Alignments of the near full length genomes, NS1, and capsid genes identified one of the five PPV6 isolates from China (98.6-99.5 % identity with the North American strains) to be the North American strains nearest relative. CONCLUSIONS: These results are the first to report the presence of PPV6 in North America and demonstrate that the virus is found in multiple geographic areas in the United States and in Mexico. The overall prevalence of PPV6 in PRRSv viremic animals is relatively low. Further, all of the PPV6 genomes found in North America are most closely related to a PPV6 strain first identified in 2014 in healthy pigs from the Tianjin province of China.

Identification of a novel Picornavirales virus distantly related to posavirus in swine feces.

De novo assembly of metagenomic sequencing reads from feces from a clinically normal pig identified two approximately 9 kb contigs which each consisted of a single large open reading frame. While one contig encoded a predicted 2990 amino acid protein with 83 % identity to the recently described posavirus 1, the other contig encoded a predicted 2942 amino acid protein with only 25 % identity limited to the genomic region encoding the RNA-dependent RNA polymerase (RdRp) of posavirus 2. Besides RdRp, search of the conserved domain database identified domains associated with picornavirus capsid proteins but failed to identify picornaviral helicase and proteinase domains. In addition, a domain representing a family of Mycoplasma and Ureaplasma immunoglobulin-blocking virulence proteins was identified near the 5'-terminus. Phylogenetic analysis found a distant relationship between this novel virus, provisionally named posavirus 3, to the unclassified posaviruses and fisavirus which are proposed to represent different genera in a novel family of the Picornavirales.

Recognition of the different structural forms of the capsid protein determines the outcome following infection with porcine circovirus type 2.

Porcine circovirus type 2 (PCV2) capsid protein (CP) is the only protein necessary for the formation of the virion capsid, and recombinant CP spontaneously forms virus-like particles (VLPs). Located within a single CP subunit is an immunodominant epitope consisting of residues 169 to 180 [CP(169-180)], which is exposed on the surface of the subunit, but, in the structural context of the VLP, the epitope is buried and inaccessible to antibody. High levels of anti-CP(169-180) activity are associated with porcine circovirus-associated disease (PCVAD). The purpose of this study was to investigate the role of the immune response to monomer CP in the development of PCVAD. The approach was to immunize pigs with CP monomer, followed by challenge with PCV2 and porcine reproductive and respiratory syndrome virus (PRRSV). To maintain the CP immunogen as a stable monomer, CP(43-233) was fused to ubiquitin (Ub-CP). Size exclusion chromatography showed that Ub-CP was present as a single 33-kDa protein. Pigs immunized with Ub-CP developed a strong antibody response to PCV2, including antibodies against CP(169-180). However, only low levels of virus neutralizing activity were detected, and viremia levels were similar to those of nonimmunized pigs. As a positive control, immunization with baculovirus-expressed CP (Bac-CP) resulted in high levels of virus neutralizing activity, small amounts of anti-CP(169-180) activity, and the absence of viremia in pigs following virus challenge. The data support the role of CP(169-180) as an immunological decoy and illustrate the importance of the structural form of the CP immunogen in determining the outcome following infection.

The Impact of Social Determinants of Health on Presentation, Treatment, and Outcomes in Branch Retinal Vein Occlusion With Cystoid Macular Edema.

BACKGROUND AND OBJECTIVE: To investigate the impact of social determinants of health on the presentation, treatment, and outcomes of branch retinal vein occlusion (BRVO) with cystoid macular edema (CME). PATIENTS AND METHODS: A retrospective chart review was conducted of patients with BRVO and CME treated with anti-vascular endothelial growth factor (anti-VEGF) injections at Atrium Health Wake Forest Baptist from 2013 to 2021. Patients' baseline characteristics including visual acuity (VA), age, sex, race, Area Deprivation Index (ADI), insurance status, baseline central macular thickness (CMT), treatment details, final VA, and final CMT were recorded. The primary outcome measure was final VA comparing more and less deprived groups, and White and non-White groups. RESULTS: Two hundred forty-four eyes of 240 patients were included. Patients with higher socioeconomic deprivation scores had thicker final CMT (P = 0.05). Non-White patients had worse presenting (P = 0.01) and final VA (P = 0.02). CONCLUSION: This study demonstrated disparities in presentation and outcomes based on socioeconomic status and race in patients with BRVO and CME treated with anti-VEGF therapy. [Ophthalmic Surg Lasers Imaging Retina 2023;54:411-416.].

Emergence of novel reassortant H3N2 swine influenza viruses with the 2009 pandemic H1N1 genes in the United States.

Reassortant H1 swine influenza viruses (SIVs) carrying 2009 pandemic H1N1 virus (pH1N1) genes have been isolated from pigs worldwide. Seven novel reassortant H3N2 SIVs were identified from diseased pigs in the USA from winter 2010 to spring 2011. These novel viruses contain three or five internal genes from pH1N1 and continue to circulate in swine herds. The emergence of novel reassortant H3N2 SIVs demonstrates reassortment between pH1N1 and endemic SIVs in pigs and justifies continuous surveillance.

Restricted enzooticity of hepatitis E virus genotypes 1 to 4 in the United States.

Hepatitis E is recognized as a zoonosis, and swine are known reservoirs, but how broadly enzootic its causative agent, hepatitis E virus (HEV), is remains controversial. To determine the prevalence of HEV infection in animals, a serological assay with capability to detect anti-HEV-antibody across a wide variety of animal species was devised. Recombinant antigens comprising truncated capsid proteins generated from HEV-subgenomic constructs that represent all four viral genotypes were used to capture anti-HEV in the test sample and as an analyte reporter. To facilitate development and validation of the assay, serum samples were assembled from blood donors (n = 372), acute hepatitis E patients (n = 94), five laboratory animals (rhesus monkey, pig, New Zealand rabbit, Wistar rat, and BALB/c mouse) immunized with HEV antigens, and four pigs experimentally infected with HEV. The assay was then applied to 4,936 sera collected from 35 genera of animals that were wild, feral, domesticated, or otherwise held captive in the United States. Test positivity was determined in 457 samples (9.3%). These originated from: bison (3/65, 4.6%), cattle (174/1,156, 15%), dogs (2/212, 0.9%), Norway rats (2/318, 0.6%), farmed swine (267/648, 41.2%), and feral swine (9/306, 2.9%). Only the porcine samples yielded the highest reactivities. HEV RNA was amplified from one farmed pig and two feral pigs and characterized by nucleotide sequencing to belong to genotype 3. HEV infected farmed swine primarily, and the role of other animals as reservoirs of its zoonotic spread appears to be limited.

Differential expression and activity of the porcine type I interferon family.

Type I interferons (IFNs) are central to innate and adaptive immunity, and many have unique developmental and physiological functions. However, in most species, only two subtypes, IFN-alpha and IFN-beta, have been well studied. Because of the increasing importance of zoonotic viral diseases and the use of pigs to address human research questions, it is important to know the complete repertoire and activity of porcine type I IFNs. Here we show that porcine type I IFNs comprise at least 39 functional genes distributed along draft genomic sequences of chromosomes 1 and 10. These functional IFN genes are classified into 17 IFN-alpha subtypes, 11 IFN-delta subtypes, 7 IFN-omega subtypes, and single-subtype subclasses of IFN-alphaomega, IFN-beta, IFN-epsilon, and IFN-kappa. We found that porcine type I IFNs have diverse expression profiles and antiviral activities against porcine reproductive and respiratory syndrome virus (PRRSV) and vesicular stomatitis virus (VSV), with activity ranging from 0 to >10(5) U.ng(-1).ml(-1). Whereas most IFN-alpha subtypes retained the greatest antiviral activity against both PRRSV and VSV in porcine and MARC-145 cells, some IFN-delta and IFN-omega subtypes, IFN-beta, and IFN-alphaomega differed in their antiviral activity based on target cells and viruses. Several IFNs, including IFN-alpha7/11, IFN-delta2/7, and IFN-omega4, exhibited minimal or no antiviral activity in the tested target cell-virus systems. Thus comparative studies showed that antiviral activity of porcine type I IFNs is virus- and cell-dependent, and IFN-alphas are positively correlated with induction of MxA, an IFN-stimulated gene. Collectively, these data provide fundamental genomic information for porcine type I IFNs, information that is necessary for understanding porcine physiological and antiviral responses.

Identification and characterization of a highly virulent triple reassortant H1N1 swine influenza virus in the United States.

A highly virulent H1N1 influenza A virus, A/Swine/Kansas/77778/2007 (KS07), which caused approximately 10% mortality in finishing pigs, was isolated from herds in the Midwestern United States. Molecular and phylogenic analysis revealed this swine isolate was a triple reassortant virus, similar to an H1N1 virus that infected humans and pigs at an Ohio county fair in August 2007. A pig challenge model was developed to evaluate the pathogenicity and transmission capacity of the KS07 virus. The results confirmed that the KS07 virus is highly virulent in pigs and easily transmitted to sentinel animals. The KS07 virus failed to cross-react with a panel of H1-specific swine sera. Interestingly, the KS07 virus shed for a prolonged period up to 7 days in infected pigs, indicating that this virus can spread efficiently between animals. The highly virulent H1N1 swine influenza virus is further evidence of reassortment among avian, human and swine influenza viruses and justifies the need for continued surveillance of influenza viruses in swine.

Fatal canine adenoviral pneumonia in two litters of Bulldogs.

Five Bulldog pups, 4 weeks of age or younger, were presented over a 2-day period for postmortem examination and diagnostic evaluation. The pups originated from 2 different litters but had been cared for at a common facility since their birth. All 5 pups died after exhibiting symptoms consisting of lethargy, dyspnea, nasal discharge, anorexia, vomiting, diarrhea, and abdominal pain. Necropsy examination revealed locally extensive to diffusely red, firm, consolidated lungs in all pups. Histopathologically, the lungs were variably effaced by multifocal areas of necrosis. The alveolar lumens contained fibrin, edema fluid, macrophages, and neutrophils. Many of the bronchioles contained cellular debris and neutrophils admixed with sloughed bronchiolar epithelium, which often contained large intranuclear amphophilic inclusion bodies that peripherally displaced chromatin. Fluorescent antibody testing was positive for Canine adenovirus. An adenovirus isolated via cell culture was positive on direct fluorescent antibody test and was identified as Canine adenovirus serotype 2 via polymerase chain reaction. Electron microscopy revealed typical viral inclusions within bronchiolar epithelial cells. Hemolytic Escherichia coli was also isolated from the lungs in 3 of the 5 pups. The current case demonstrates a natural and rare fatal infection with a viral agent that is typically associated with immunosuppression in both animals and humans.

Assessing the effects of medium-chain fatty acids and fat sources on PEDV infectivity.

The overall objective of this study was to compare the efficacy of medium-chain fatty acids (MCFA) to other common fat sources to minimize the risk of porcine epidemic diarrhea virus (PEDV) cross-contamination in a pig bioassay. Treatments were feed with mitigants inoculated with PEDV after application and were: 1) positive control with no chemical treatment; 2) 0.325% commercially available formaldehyde-based product; 3) 1% blend of 1:1:1 caproic (C6), caprylic (C8), and capric acids (C10) and applied with an aerosolizing nozzle; 4) treatment 3 applied directly into the mixer without an aerosolizing nozzle; 5) 0.66% caproic acid; 6) 0.66% caprylic acid; 7) 0.66% capric acid; 8) 0.66% lauric acid; 9) 1% blend of 1:1 capric and lauric acids; 10) 0.3% commercially available dry C12 product; 11) 1% canola oil; 12) 1% choice white grease; 13) 2% coconut oil; 14) 1% coconut oil; 15) 2% palm kernel oil; 16) 1% palm kernel oil; 17) 1% soy oil and four analysis days (0, 1, 3, and 7 post inoculation) as well as 1 treatment of PEDV-negative feed without chemical treatment. There was a treatment × day interaction (P < 0.002) for detectable PEDV RNA. The magnitude of the increase in Ct value from d 0 to 7 was dependent upon the individual treatments. Feed treated with individual MCFA, 1% MCFA blend, or commercial-based formaldehyde had fewer (P < 0.05) detectable viral particles than all other treatments. Commercial-based formaldehyde, 1% MCFA, 0.66% caproic, 0.66% caprylic, and 0.66% capric acids had no evidence of infectivity 10-d old pig bioassay, while there was no evidence the C12 commercial product or longer chain fat sources inhibited PEDV infectivity. Interestingly, pigs given the coconut oil source with the highest composition of caprylic and capric only showed signs of infectivity on the last day of bioassay. These data suggest some MCFA have potential for reducing post feed manufacture PEDV contamination.

A field evaluation of mortality rate and growth performance in pigs vaccinated against porcine circovirus type 2.

OBJECTIVE: To evaluate, under field conditions, the effects of a commercial porcine circovirus type 2 (PCV2) vaccine on mortality rate and growth performance in a herd infected with PCV2 that had a history of porcine circovirus disease. DESIGN: Randomized controlled clinical trial. ANIMALS: 485 commercial, cross-bred, growing pigs. PROCEDURES: Prior to weaning, pigs were randomly assigned within litter to a vaccination or unvaccinated control group. Pigs in the vaccination group were given a commercial PCV2 vaccine at weaning and 3 weeks later. Mortality rate was recorded, and pigs were weighed prior to vaccination, when moved from the nursery, and prior to marketing. Infection status was assessed by serologic testing and detection of viral DNA in serum. RESULTS: Compared with control pigs, pigs vaccinated against PCV2 had a significantly lower mortality rate during the finishing phase, significantly higher average daily gain during the finishing phase, and significantly lower likelihood of being lightweight at the time of marketing. For vaccinated pigs, overall mortality rate was reduced by 50% and average daily gain during the finishing period was increased by 9.3%. At the time of marketing, vaccinated pigs weighed an average of 8.8 kg (19.4 lb) more than control pigs, without any difference in days to marketing. Serum PCV2 antibody titers increased in control pigs, and PCV2 DNA was detected, indicating active PCV2 infection. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that vaccination against PCV2 was effective at reducing mortality rate and improving growth performance among pigs in a herd infected with PCV2.

Molecular detection and characterization of transient bovine viral diarrhea virus (BVDV) infections in cattle commingled with ten BVDV persistently infected cattle.

Fifty-three cattle of unknown serologic status that were not persistently infected (PI) with bovine viral diarrhea virus (BVDV) were commingled with 10 cattle that were PI with different strains of BVDV, and were monitored for an extended commingle period using a reverse-transcription real-time PCR (RT-rtPCR) BVDV assay on various sample types. Transient infections with BVDV were also assessed by virus isolation, virus neutralization (VN) assays, and direct buffy coat 5'-UTR sequencing. Infections were demonstrated in all cattle by RT-rtPCR; however, the detection rate was dependent on the type of sample. Buffy coat samples demonstrated a significantly greater number of positive results ( p ≤ 0.05) than either serum or nasal swab samples. Presence of elevated BVDV VN titers at the onset inversely correlated with the number of test days positive that an individual would be identified by RT-rtPCR from buffy coat samples, and directly correlated with the average Ct values accumulated over all RT-rtPCR test days from buffy coat samples. Both single and mixed genotype/subgenotype/strain infections were detected in individual cattle by direct sample 5'-UTR sequencing. A BVDV-2a strain from a PI animal was found to be the predominant strain infecting 64% of all non-PI cattle; BVDV-1b strains originating from 3 PI cattle were never detected in non-PI cattle. Although direct sample 5'-UTR sequencing was capable of demonstrating mixed BVDV infections, identifying all strains suspected was not always efficient or possible.

Fecal Microbiota Transplantation Is Associated With Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease.

Porcine circovirus associated disease (PCVAD) is a term used to describe the multi-factorial disease syndromes caused by porcine circovirus type 2 (PCV-2), which can be reproduced in an experimental setting through the co-infection of pigs with PCV-2 and porcine reproductive and respiratory syndrome virus (PRRSV). The resulting PCVAD-affected pigs represent a subpopulation within the co-infected group. In co-infection studies, the presence of increased microbiome diversity is linked to a reduction in clinical signs. In this study, fecal microbiota transplantation (FMT) was investigated as a means to prevent PCVAD in pigs co-infected with PRRSV and PCV-2d. The sources of the FMT material were high-parity sows with a documented history of high health status and robust litter characteristics. The analysis of the donated FMT material showed the absence of common pathogens along with the presence of diverse microbial phyla and families. One group of pigs (n = 10) was administered the FMT while a control group (n = 10) was administered a sterile mock-transplant. Over the 42-day post-infection period, the FMT group showed fewer PCVAD-affected pigs, as evidenced by a significant reduction in morbidity and mortality in transplanted pigs, along with increased antibody levels. Overall, this study provides evidence that FMT decreases the severity of clinical signs following co-infection with PRRSV and PCV-2 by reducing the prevalence of PCVAD.

Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus.

Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n=126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV.