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DNA methylation is a form of epigenetic regulation, having pivotal parts in controlling cellular expansion and expression levels within genes. Although blood DNA methylation has been studied in humans and other species, its prominence in cattle is largely unknown. This study aimed to methodically probe the genomic methylation map of Xinjiang brown (XJB) cattle suffering from bovine respiratory disease (BRD), consequently widening cattle blood methylome ranges. Genome-wide DNA methylation profiling of the XJB blood was investigated through whole-genome bisulfite sequencing (WGBS). Many differentially methylated regions (DMRs) obtained by comparing the cases and controls groups were found within the CG, CHG, and CHH (where H is A, T, or C) sequences (16,765, 7502, and 2656, respectively), encompassing 4334 differentially methylated genes (DMGs). Furthermore, GO/KEGG analyses showed that some DMGs were involved within immune response pathways. Combining WGBS-Seq data and existing RNA-Seq data, we identified 71 significantly differentially methylated (DMGs) and expressed (DEGs) genes (p < 0.05). Next, complementary analyses identified nine DMGs (LTA, STAT3, IKBKG, IRAK1, NOD2, TLR2, TNFRSF1A, and IKBKB) that might be involved in the immune response of XJB cattle infected with respiratory diseases. Although further investigations are needed to confirm their exact implication in the involved immune processes, these genes could potentially be used for a marker-assisted selection of animals resistant to BRD. This study also provides new knowledge regarding epigenetic control for the bovine respiratory immune process.

Alterations of the lung microbiota (LM) are associated with clinical features in chronic lung diseases (CLDs) with growing evidence that an altered LM contributes to the pathogenesis of such disorders. The common use of antimicrobial drugs in the management of CLDs likely represents a confounding factor in the study of the LM. The aim of the present study was to assess the effect of oral administration of amoxicillin/clavulanic acid (AC) on the LM in healthy dogs (n = 6) at short (immediately after stopping AC [D10]) and medium-term (16 days after stopping AC [D26]). Metagenetic analyses were performed on the V1–V3 hypervariable region of 16S rDNA after extraction of total bacterial DNA from samples of bronchoalveolar lavage fluid (BALF). AC did not induce significant changes in BALF cellular counts or in the bacterial load or microbial richness, evenness and α-diversity, while the β-diversity was clearly modified at D10 compared with D0 (before AC administration) and D26 (P < 0.01). The relative abundance of Bacteroidetes and Proteobacteria increased at D10 (P < 0.01) in comparison with D0 and D26 (P < 0.01). The relative abundance of Firmicutes decreased from D0 to D10 (P < 0.01) and increased from D10 to D26 (P < 0.01), but was still lower than at D0 (P < 0.01). The proportion of Actinobacteria increased at D26 compared with D0 and D10 (P < 0.01). Significant differences between timepoints at the level of family, genus or species were not found. In conclusion, in healthy dogs, oral administration of AC induces significant changes in LM at the phyla level and in the β-diversity. Most changes normalize within 2 weeks after discontinuation of AC.

The objective of this work was the evaluation of the meat production and laying performances, and the meat and egg quality of two breeds of Vietnamese broiler chickens, Ho and Dong Tao, fed on a commercial diet. In a survey, we continuously recorded for 28 weeks, the data on the production performance and meat quality of 250 chicks from each breed. We investigated egg laying and egg quality using 36 Ho and 32 Dong Tao hens during 52 weeks of laying. The growth patterns were similar for the two breeds. Feed conversion ratios were also similar, and demonstrated the low efficiency of these two breeds when compared to commercial broilers. Slaughter age proved to affect several carcass yield characteristics, showing that slaughtering between 16 and 20 weeks might be better than at the usual age of 28 weeks. Yield, carcass composition and meat quality differed between the two studied breeds. The eggs production and number of embryonated eggs were low for the two breeds when compared to other breeds, with a lower hatching performance in Ho than in Dong Tao. In summary, the production performances of Ho and Dong Tao chickens were low, even when birds were fed a commercial diet. The study demonstrates the need to find ways to improve the production and reproduction performances of these animals, in order to contribute to the program of conservation and exploitation of these two breeds.

Serum triglyceride concentrations increase in dogs with obesity, which is typically assessed by body condition score (BCS), however little is known about changes that take place in non-obese dogs in overweight condition. Further, the associations of triglyceride levels with other markers of energy homeostasis are poorly characterised in healthy animals. The present study aimed to evaluate associations between both BCS and triglyceride concentrations with other markers of lipid and glucose metabolism in healthy, non-obese dogs, as well as to assess whether these markers change significantly in non-obese dogs with overweight as compared to their lean counterparts. Serum concentrations of cholesterol, free fatty acids, triglycerides, insulin, glucose and fructosamine were measured in 532 healthy, client-owned dogs, assigned either to ‘lean’ (BCS: 3–5) or ‘overweight’ (BCS: 6–7) categories. Generalised linear mixed models were used to assess associations between BCS categories, triglyceride concentrations and other variables, correcting for the effect of breed. Compared with lean dogs, overweight dogs had a greater serum cholesterol concentration (95% CI, 5.3–6.2 mmol/L or 205–237 mg/dL versus 5.1–5.4 mmol/L or 198–210 mg/dL, p = 0.0032), insulin concentration (95% CI, 17.5–22.1 μU/ml versus 16.7–18.0 μU/ml, p = 0.0374) and were older (95% CI, 4.0–5.3 versus 3.4–3.7 years, p = 0.0005). Triglyceride concentrations were positively associated with fructosamine (r2 = 0.31, p = 0.0012), cholesterol (r2 = 0.25, p

Striped catfish (Pangasianodon hypophthalmus), a freshwater species cultured mainly in the Mekong Delta region in Southern Vietnam, is facing a significant challenge due to salinity intrusion as a result of climatic changes. Given these evolving environmental conditions, selecting new strains with a higher salinity tolerance could make production of striped catfish economically feasible in brackish environments. In this study, we carried out a selection program aimed at developing a striped catfish strain able to survive and grow fast in a saline environment. To implement the selection program, we first collected males and females from different provinces in the Mekong delta. We next performed a factorial cross of these breeders to produce half- and full-sib families. When fish reached fry stage (47 dph), we put them in a saline environment (10 ppt) and subsequently kept 50 % of the fastest-growing fish after 143 days post hatching (dph). We repeated this mass selection procedure after 237 dph and 340 dph. We maintained in parallel a randomly selected group in saline conditions and a group of fish reared in freshwater to serve as controls. After crossing the selected individuals, we performed several tests on the next generation of fish to evaluate the effectiveness of selection after one generation in saline conditions. Average direct responses to selection were 18.0 % for growth and 11.4 % for survival rate after one generation of selection. We estimated a moderate realized heritability (0.29) for body weight. The genetic gains obtained in our study for body weight and survival rate after one generation of selection under saline conditions suggest that selection can be effective to improve ability of striped catfish to cope with saline stress. We conclude that our selection program has succeeded in developing a productive strain of striped catfish with better tolerance to salinity.

(1) Idiopathic epilepsy (IE) is thought to have a genetic cause in several dog breeds. However, only two causal variants have been identified to date, and few risk loci are known. No genetic studies have been conducted on IE in the Dutch partridge dog (DPD), and little has been reported on the epileptic phenotype in this breed. (2) Owner-filled questionnaires and diagnostic investigations were used to characterize IE in the DPD. A genome-wide association study (GWAS) involving 16 cases and 43 controls was performed, followed by sequencing of the coding sequence and splice site regions of a candidate gene within the associated region. Subsequent whole-exome sequencing (WES) of one family (including one IE-affected dog, both parents, and an IE-free sibling) was performed. (3) IE in the DPD has a broad range in terms of age at onset, frequency, and duration of epileptic seizures. Most dogs showed focal epileptic seizures evolving into generalized seizures. A new risk locus on chromosome 12 (BICF2G630119560; praw = 4.4 × 10−7; padj = 0.043) was identified through GWAS. Sequencing of the GRIK2 candidate gene revealed no variants of interest. No WES variants were located within the associated GWAS region. However, a variant in CCDC85A (chromosome 10; XM_038680630.1: c.689C > T) was discovered, and dogs homozygous for the variant (T/T) had an increased risk of developing IE (OR: 6.0; 95% CI: 1.6–22.6). This variant was identified as likely pathogenic according to ACMG guidelines. (4) Further research is necessary before the risk locus or CCDC85A variant can be used for breeding decisions.

Abstract Background Two-dimensional speckle tracking (2DST) technique has been validated in numerous animal species, but neither studies of repeatability nor measurements after exercise or in animals with cardiac disease have been reported in goats. Goats are an attractive candidate for animal models in human cardiology because they are easy to handle and have a body and heart size comparable to that of humans. Therefore, the aim of this study was to validate this technique in goats for further clinical and experimental applications in this species. Results This study was divided into several steps. First, a standardized echocardiographic protocol was performed and 5 cineloops of a right parasternal short-axis view at papillary muscles level were recorded three times at one-day intervals in ten healthy adult unsedated Saanen goats to test repeatability and variability of 2DST measurements. Then, the same measurements were performed immediately before and after a standardized exercise on treadmill in seven of the goats, and at 24 h after induction of an experimental ischemic cardiomyopathy in five of the goats, to test the reliability of the technique to assess physiological and pathological changes. Average and regional measurements of radial and circumferential strain and strain rate, radial displacement, rotation and rotation rate were obtained. Comparisons were performed using two-way ANOVA (p

Myeloperoxidase (MPO), as a marker of neutrophil activation, has been associated with equine endometritis. However, in absence of inflammation, MPO is constantly detected in the uterine lumen of estrous mares. The aim of this study was to characterize MPO in the uterus of mares under physiological conditions as a first step to better understand the role of this enzyme in equine reproduction. Total and active MPO concentrations were determined, by ELISA and SIEFED assay, respectively, in low-volume lavages from mares in estrus (n = 26), diestrus (n = 18) and anestrus (n = 8) in absence of endometritis. Immunohistochemical analysis was performed on 21 endometrial biopsies randomly selected: estrus (n = 11), diestrus (n = 6) and anestrus (n = 4). MPO, although mostly enzymatically inactive, was present in highly variable concentrations in uterine lavages in all studied phases, with elevated concentrations in estrus and anestrus, while in diestrus, concentrations were much lower. Intracytoplasmic immunoexpression of MPO was detected in the endometrial epithelial cells, neutrophils and glandular secretions. Maximal expression was observed during estrus in mid and basal glands with a predominant intracytoplasmic apical reinforcement. In diestrus, immunopositive glands were sporadic. In anestrus, only the luminal epithelium showed residual MPO immunostaining. These results confirm a constant presence of MPO in the uterine lumen of mares in absence of inflammation, probably as part of the uterine mucosal immune system, and suggest that endometrial cells are a source of uterine MPO under physiological cyclic conditions.

Functional diversity of tissue-resident macrophages and signals governing their ontogeny and turnover remain unknown for the majority of tissues. Here the authors describe two phenotypically and functionally distinct long-lived populations of lung interstitial macrophages and their putative blood-derived monocytic precursor.

Abstract Background Despite the successful mapping of genes involved in the determinism of numerous traits, a large part of the genetic variation remains unexplained. A possible explanation is that the simple models used in many studies might not properly fit the actual underlying situations. Consequently, various methods have attempted to deal with the simultaneous mapping of genomic regions, assuming that these regions might interact, leading to a complex determinism for various traits. Despite some successes, no gold standard methodology has emerged. Actually, combining several interaction mapping methods might be a better strategy, leading to positive results over a larger set of situations. Our work is a step in that direction. Results We first have demonstrated why aggregating results from several distinct methods might increase the statistical power while controlling the type I error. We have illustrated the approach using 6 existing methods (namely: MDR, Boost, BHIT, KNN-MDR, MegaSNPHunter and AntEpiSeeker) on simulated and real data sets. We have used a very simple aggregation strategy: a majority vote across the best loci combinations identified by the individual methods. In order to assess the performances of our aggregation approach in problems where most individual methods tend to fail, we have simulated difficult situations where no marginal effects of individual genes exist and where genetic heterogeneity is present. we have also demonstrated the use of the strategy on real data, using a WTCCC dataset on rheumatoid arthritis. Since we have been using simplistic assumptions to infer the expected power of the aggregation method, the actual power we estimated from our simulations has turned out to be a bit smaller than theoretically expected. Results nevertheless have shown that grouping the results of several methods is advantageous in terms of power, accuracy and type I error control. Furthermore, as more methods should become available in the future, using a grouping strategy will become more advantageous since adding more methods seems to improve the performances of the aggregated method. Conclusions The aggregation of methods as a tool to detect genetic interactions is a potentially useful addition to the arsenal used in complex traits analyses.

Summary: In the context of the SARS-CoV-2 pandemic, reuse of surgical masks and filtering facepiece respirators has been recommended. Their reuse necessitates procedures to inactivate contaminating human respiratory and oral pathogens. We previously demonstrated decontamination of masks and respirators contaminated with an infectious SARS-CoV-2 surrogate via ultraviolet germicidal irradiation, vaporised hydrogen peroxide, and use of dry heat. Here, we show that these same methods efficiently inactivate a more resistant, non-enveloped oral virus; decontamination of infectious murine norovirus-contaminated masks and respirators reduced viral titres by over four orders of magnitude on mask or respirator coupons.

The aim of this study was to obtain the growth parameters of specific spoilage micro-organisms previously isolated in minced pork (MP) samples and to develop a three-spoilage species interaction model under different storage conditions. Naturally contaminated samples were used to validate this approach by considering the effect of the food microbiota. Three groups of bacteria were inoculated on irradiated samples, in mono- and in co-culture experiments (n = 1152): Brochothrix thermosphacta, Leuconostoc gelidum, and Pseudomonas spp. (Pseudomonas fluorescens and Pseudomonas fragi). Samples were stored in two food packaging [food wrap and modified atmosphere packaging (CO2 30%/O2 70%)] at three isothermal conditions (4, 8, and 12°C). Analysis was carried out by using both 16S rRNA gene amplicon sequencing and classical microbiology in order to estimate bacterial counts during the storage period. Growth parameters were obtained by fitting primary (Baranyi) and secondary (square root) models. The food packaging shows the highest impact on bacterial growth rates, which in turn have the strongest influence on the shelf life of food products. Based on these results, a three-spoilage species interaction model was developed by using the modified Jameson-effect model and the Lotka Volterra (prey–predator) model. The modified Jameson-effect model showed slightly better performances, with 40–86% out of the observed counts falling into the Acceptable Simulation Zone (ASZ). It only concerns 14–48% for the prey–predator approach. These results can be explained by the fact that the dynamics of experimental and validation datasets seems to follow a Jameson behavior. On the other hand, the Lotka Volterra model is based on complex interaction factors, which are included in highly variable intervals. More datasets are probably needed to obtained reliable factors, and so better model fittings, especially for three- or more-spoilage species interaction models. Further studies are also needed to better understand the interaction of spoilage bacteria between them and in the presence of natural microbiota.

Although several studies have focused on the dynamics of bacterial food community, little is known about the variability of batch production and microbial changes that occur during storage. The aim of the study was to characterize the microbial spoilage community of minced pork meat samples, among different food production and storage, using both 16S rRNA gene sequencing and classical microbiology. Three batches of samples were obtained from four local Belgian facilities (A–D) and stored until shelf life under food wrap (FW) and modified atmosphere packaging (MAP, CO2 30%/O2 70%), at constant and dynamic temperature. Analysis of 288 samples were performed by 16S rRNA gene sequencing in combination with counts of psychrotrophic and lactic acid bacteria at 22°C. At the first day of storage, different psychrotrophic counts were observed between the four food companies (Kruskal-Wallist test, p-value < 0.05). Results shown that lowest microbial counts were observed at the first day for industries D and A (4.2 ± 0.4 and 5.6 ± 0.1 log CFU/g, respectively), whereas industries B and C showed the highest results (7.5 ± 0.4 and 7.2 ± 0.4 log CFU/g). At the end of the shelf life, psychrotrophic counts for all food companies was over 7.0 log CFU/g. With metagenetics, 48 OTUs were assigned. At the first day, the genus Photobacterium (86.7 and 19.9% for food industries A and C, respectively) and Pseudomonas (38.7 and 25.7% for food companies B and D, respectively) were dominant. During the storage, a total of 12 dominant genera (>5% in relative abundance) were identified in MAP and 7 in FW. Pseudomonas was more present in FW and this genus was potentially replaced by Brochothrix in MAP (two-sided Welch’s t-test, p-value < 0.05). Also, a high Bray-Curtis dissimilarity in genus relative abundance was observed between food companies and batches. Although the bacteria consistently dominated the microbiota in our samples are known, results indicated that bacterial diversity needs to be addressed on the level of food companies, batches variation and food storage conditions. Present data illustrate that the combined approach provides complementary results on microbial dynamics in minced pork meat samples, considering batches and packaging variations.

Abstract Background Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods. Results When using 600 K single nucleotide polymorphisms (SNPs), the inbreeding coefficient (probability of sampling an HBD locus in an individual) was on average 0.303 (ranging from 0.258 to 0.375). HBD-classes associated to historical ancestors (with small segments ≤ 200 kb) accounted for 21.6% of the genome length (71.4% of the total length of the genome in HBD segments), whereas classes associated to more recent ancestors accounted for only 22.6% of the total length of the genome in HBD segments. However, these recent classes presented more individual variation than more ancient classes. Although inbreeding coefficients obtained with low SNP densities (7 and 32 K) were much lower (0.060 and 0.093), they were highly correlated with those obtained at higher density (r = 0.934 and 0.975, respectively), indicating that they captured most of the individual variation. At higher SNP density, smaller HBD segments are identified and, thus, more past generations can be explored. We observed very high correlations between our estimates and those based on homozygosity (r = 0.95) or on runs-of-homozygosity (r = 0.95). As expected, pedigree-based estimates were mainly correlated with recent HBD-classes (r = 0.56). Conclusions Although we observed high levels of autozygosity associated with small HBD segments in BBB cattle, recent inbreeding accounted for most of the individual variation. Recent autozygosity can be captured efficiently with low-density SNP arrays and relatively simple models (e.g., two HBD classes). The HMM framework provides local HBD probabilities that are still useful at lower SNP densities.

We report the detection of Moku virus in invasive Asian hornets (Vespa velutina nigrithorax) in Belgium. This constitutes an unexpected report of this iflavirus outside Hawaii, USA, where it was recently described in social wasps. Although virulence of Moku virus is unknown, its potential spread raises concern for European honeybee populations.

This survey, conducted with 461 racehorse owners-breeders in Algeria between 2009 and 2011, investigates their perceptions, objectives and practices regarding selective breeding. Racehorse breeding is a full-time professional activity for a third of interviewees. The holdings are small-sized with 77% owning one or two mares. The regular practice of mating is here used to categorize breeders according to their degree of professionalization (38.4% professional vs. 61.6% occasional breeders). Experience in the sector was also used to classify breeders, considering as "junior" the breeders under 10 years experience (38.8%) and as "senior" those above 10 years (61.2%). More than professionalization, experience shows a significant impact on practices and objectives. Thus, experience influences breed choice (junior breeders tend to specialize while senior own both Arabian and Thoroughbreds), age at first foaling (sooner among senior breeders), information sources considered for selecting stallions (senior use more diversified sources), the importance granted to the price of mating (greater for junior breeders), the importance granted to the ranking compared to earnings (the ranking being more important to junior breeders), and the priority given to breeding (junior breeders give higher priority to a buy-race-resell activity). Finally, racehorse breeding is poorly professionalized, the only financial goal being cost coverage. Despite inappropriate practices, an interest for selection is noticed.

For the last twenty years, the consumption of poultry meat has boomed in Vietnam as in the rest of the developing world. Capital-intensive production has grown rapidly to satisfy this demand. Based on a few numbers of genetically uniform strains, these systems threaten biodiversity. In Vietnam, both rural and urban households still keep indigenous chickens as part of a diversified livelihood portfolio. In line with the national in situ conservation strategy, this study approached the context of local poultry keeping in two rural and one suburban districts of Northern Vietnam. It aimed at understanding households’ willingness, constraints and opportunities for practice improvement, including breeds’ management. As the Ri chicken constitutes the large majority of backyard flocks, two particular objectives of this study are the morpho-biometric characterisation of phenotypic diversity among individuals classified as Ri by farmers and an assessment of their productive potential. Chicken was found to hold a different place in livelihoods of the three districts with consequences on the management of genetic resources. The most favourable conditions for improvement of the Ri breed was found in the rural district of Luong-Son, due to market integration. In the more remote district of Ky-Son, living standards were lower and much would be gained from Ri conservation. Ri breed was the most threatened in the suburban Gia-Lam district, where poultry was a minor side-activity, lacking incentive for genetic management. From motives and constraints, tracks about breeding goals are suggested. Further considerations about conservation, improvement, market integration and livelihoods are proposed.

Cyprinid herpesvirus 3 (CyHV 3) is causing severe economic losses worldwide in common and koi carp industries, and a safe and efficacious attenuated vaccine compatible with mass vaccination is needed. We produced single deleted recombinants using prokaryotic mutagenesis. When producing a recombinant lacking open reading frame 134 (ORF134), we unexpectedly obtained a clone with additional deletion of ORF56 and ORF57. This triple deleted recombinant replicated efficiently in vitro and expressed an in vivo safety/efficacy profile compatible with use as an attenuated vaccine. To determine the role of the double ORF56-57 deletion in the phenotype and to improve further the quality of the vaccine candidate, a series of deleted recombinants was produced and tested in vivo. These experiments led to the selection of a double deleted recombinant lacking ORF56 and ORF57 as a vaccine candidate. The safety and efficacy of this strain were studied using an in vivo bioluminescent imaging system (IVIS), qPCR, and histopathological examination, which demonstrated that it enters fish via skin infection similar to the wild type strain. However, compared to the parental wild type strain, the vaccine candidate replicated at lower levels and spread less efficiently to secondary sites of infection. Transmission experiments allowing water contamination with or without additional physical contact between fish demonstrated that the vaccine candidate has a reduced ability to spread from vaccinated fish to naïve sentinel cohabitants. Finally, IVIS analyses demonstrated that the vaccine candidate induces a protective mucosal immune response at the portal of entry. Thus, the present study is the first to report the rational development of a recombinant attenuated vaccine against CyHV 3 for mass vaccination of carp. We also demonstrated the relevance of the CyHV 3 carp model for studying alloherpesvirus transmission and mucosal immunity in teleost skin.

The callipyge phenotype is an ovine muscular hypertrophy characterized by polar overdominance: only heterozygous +Mat/CLPGPat animals receiving the CLPG mutation from their father express the phenotype. +Mat/CLPGPat animals are characterized by postnatal, ectopic expression of Delta-like 1 homologue (DLK1) and Paternally expressed gene 11/Retrotransposon-like 1 (PEG11/RTL1) proteins in skeletal muscle. We showed previously in transgenic mice that ectopic expression of DLK1 alone induces a muscular hypertrophy, hence demonstrating a role for DLK1 in determining the callipyge hypertrophy. We herein describe newly generated transgenic mice that ectopically express PEG11 in skeletal muscle, and show that they also exhibit a muscular hypertrophy phenotype. Our data suggest that both DLK1 and PEG11 act together in causing the muscular hypertrophy of callipyge sheep.

Alcelaphine herpesvirus 1 (AlHV-1), carried by wildebeest asymptomatically, causes malignant catarrhal fever (WD-MCF) when cross-species transmitted to a variety of susceptible species of the Artiodactyla order. Experimentally, WD-MCF can be induced in rabbits. The lesions observed are very similar to those described in natural host species. Here, we used the rabbit model and in vivo 5-Bromo-2'-Deoxyuridine (BrdU) incorporation to study WD-MCF pathogenesis. The results obtained can be summarized as follows. (i) AlHV-1 infection induces CD8(+) T cell proliferation detectable as early as 15 days post-inoculation. (ii) While the viral load in peripheral blood mononuclear cells remains below the detection level during most of the incubation period, it increases drastically few days before death. At that time, at least 10% of CD8(+ )cells carry the viral genome; while CD11b(+), IgM(+) and CD4(+) cells do not. (iii) RT-PCR analyses of mononuclear cells isolated from the spleen and the popliteal lymph node of infected rabbits revealed no expression of ORF25 and ORF9, low or no expression of ORF50, and high or no expression of ORF73. Based on these data, we propose a new model for the pathogenesis of WD-MCF. This model relies on proliferation of infected CD8(+) cells supporting a predominantly latent infection.

To identify novel susceptibility loci for Crohn disease (CD), we undertook a genome-wide association study with more than 300,000 SNPs characterized in 547 patients and 928 controls. We found three chromosome regions that provided evidence of disease association with p-values between 10(-6) and 10(-9). Two of these (IL23R on Chromosome 1 and CARD15 on Chromosome 16) correspond to genes previously reported to be associated with CD. In addition, a 250-kb region of Chromosome 5p13.1 was found to contain multiple markers with strongly suggestive evidence of disease association (including four markers with p < 10(-7)). We replicated the results for 5p13.1 by studying 1,266 additional CD patients, 559 additional controls, and 428 trios. Significant evidence of association (p < 4 x 10(-4)) was found in case/control comparisons with the replication data, while associated alleles were over-transmitted to affected offspring (p < 0.05), thus confirming that the 5p13.1 locus contributes to CD susceptibility. The CD-associated 250-kb region was saturated with 111 SNP markers. Haplotype analysis supports a complex locus architecture with multiple variants contributing to disease susceptibility. The novel 5p13.1 CD locus is contained within a 1.25-Mb gene desert. We present evidence that disease-associated alleles correlate with quantitative expression levels of the prostaglandin receptor EP4, PTGER4, the gene that resides closest to the associated region. Our results identify a major new susceptibility locus for CD, and suggest that genetic variants associated with disease risk at this locus could modulate cis-acting regulatory elements of PTGER4.