Helicobacter pylori Cytotoxin-Associated Gene A (cagA) and Vacuolating Cytotoxin Gene A (vacA) Genotypes in Gastrointestinal Patients From Central Thailand.

Introduction The development of diseases associated with Helicobacter pylori (H. pylori) infection is closely linked to its virulence genes, which vary by geographic region. This study aimed to determine the prevalence of H. pylori cytotoxin-associated gene A (cagA) and vacuolating cytotoxin gene A (vacA) genes and their genotypes in patients with gastrointestinal diseases. Methods Patients diagnosed with gastrointestinal disease based on endoscopic findings were recruited for the study. Gastric biopsies were collected to screen for H. pylori infection using polymerase chain reaction (PCR). Subsequently, infected samples were tested for cagA and vacA genes, and their genotypes were analyzed by sequencing. Results Among 250 cases, 56% (140/250) exhibited gastrointestinal diseases. Of these cases, 32.1% (45/140) were infected with H. pylori. Regarding gene detection, 40 (88.9%) samples were positive for cagA, while all samples were positive for vacA. For cagA, the Western type with the ABC pattern was the most prominent. There was a statistically significant association between cagA genotypes and clinical outcomes, with the Western type being more prevalent in gastritis patients. For vacA, there was a high prevalence of the s1 and i1, while the m1 and m2 showed similar prevalence. In our combined analysis, the dominant vacA genotype combinations were s1m1i1 (46.7%). There were no statistical differences between the vacA genotypes and clinical outcomes (P > 0.05). Conclusion This study revealed a high prevalence of H. pylori cagA and vacA genes, but there were variations in their genotypes. A correlation was observed between the Western-type cagA and gastritis; however, no association was found between vacA genotypes and clinical outcomes.

Morphometrical and molecular identification of Echinococcus granulosus genotypes in wild canids in north of Iran.

BACKGROUND/OBJECTIVE: The cestode Echinococcus granulosus causes cystic echinococcosis, a zoonotic parasitic infection that constitutes a significant public health risk. This parasite has been documented to have potential reservoirs and carriers among wild canids, namely wolves, foxes and jackals. This study aimed to determine the prevalence and molecular characteristics of E. granulosus sensu lato species/genotypes among wild canids in three northern, northeastern and north-western Iran regions. METHODS: From 2019 to 2022, 93 wild canid carcasses (69 jackals), (22 foxes) and (2 wolves) were collected that were killed in car accidents or illnesses. Analyses of morphology and morphometry were performed to verify the presence of E. granulosus. To determine E. granulosus s.l. species/genotypes, polymerase chain reaction (PCR)-RFLP (ITS1) was performed utilizing the Bsh1236I (BstUI) restriction enzyme. COX1, NADH1 and ITS1 gene sequencing were also performed to confirm the PCR-RFLP results. RESULTS: During this study, 93 wild canids were examined, and 3.2% (95% CI: 0%-7%) of the 93 were infected with Echinococcus. The north-western region of Iran showed two out of 30 jackals (6.6%) infected with adult Echinococcus compared to one out of 35 jackals (2.8%) in the northern region. DNA from Echinococcus was detected in these individuals by PCR. Based on PCR-RFLP analysis of the ITS1 gene and sequencing of COX1, NADH1 and ITS1 gene, E. granulosus sensu stricto genotype was confirmed in the jackals that had been infected. CONCLUSION: Evidence shows that E. granulosus occurs in jackals in Iran, with the E. granulosus s.s. genotype being the most common. This parasite has been identified as a zoonotic parasite with a genotype that can be transmitted to livestock and humans. Establishing effective control measures to prevent the spread of echinococcosis and ensure public health is crucial.

Prevalence and genotype distribution of human papillomavirus infection among 66000 women from 2014 to 2023 in the plateau region of Southwest China.

BACKGROUND: Persistent infection with high-risk human papillomavirus (HR-HPV) plays a key role in the onset of cervical cancer. This study was designed to examine the epidemiological trends and genotype distribution of HPV from 2014 to 2023 in the plateau region of Southwest China. METHODS: The findings could offer valuable insights for clinical screening of cervical cancer and the formulation of HPV vaccination policies. This retrospective study analyzed 66,000 women who received HPV-DNA testing at the First People's Hospital of Qujing, Yunnan, China, between 2014 and 2023. The cohort consisted of 33,512 outpatients, 3,816 inpatients, and 28,672 individuals undergoing health examinations. Cervical cells were collected for DNA extraction, and PCR amplification along with Luminex xMAP technology were used to detect 27 HPV genotypes. The data analysis was conducted using GraphPad Prism and IBM SPSS Statistics 27 software. RESULTS: The overall HPV infection rate at the First People's Hospital of Qujing declined from 24.92% in 2014 to 16.29% in 2023, averaging 16.02%. Specific infection rates were 18.50% among outpatients, 12.97% among inpatients, and 13.53% for health examination attendees. The predominant high-risk HPV genotypes identified were HPV52 (2.61%), HPV16 (2.06%), HPV58 (1.81%), HPV53 (1.55%), and HPV39 (1.09%). Meanwhile, the most frequent low-risk HPV genotypes were HPV6 (1.30%), HPV61 (1.21%), and HPV11 (0.85%). In HPV-positive cases, the distribution of single, double, triple, and quadruple or more infections were 79.90%, 15.17%, 3.59%, and 1.33%, respectively. The proportions of pure LR-HPV, pure HR-HPV, and mixed infections were 22.16%, 67.82%, and 10.02%, respectively. Age-specific analysis revealed a bimodal distribution of HPV infection, with the infection rate rapidly decreasing from 44.02% in the ≤ 19 age group to 19.55% in the 20-29 age group and 13.84% in the 30-39 age group, followed by a gradual increase to 14.64% in the 40-49 age group, 16.65% in the 50-59 age group, and 22.98% in the ≥ 60 age group. The coverage rates of the three available vaccines are all below 50%. The results of this study indicated a declining trend in HPV prevalence in the plateau region of Southwest China over the period from 2014 to 2023, especially in the reduction of genotypes targeted by vaccines. CONCLUSION: There were significant variations in the genotypes prevalent among different age groups, years, and patient sources within the same region. The underwhelming vaccination rates emphasize the critical need for developing either a multivalent vaccine or a personalized vaccine that targets the HPV genotypes common in the Chinese population. Furthermore, vaccinating adolescents to curb HPV infection and ensuring regular cervical cancer screenings for postmenopausal women are crucial steps.

Stress response in tomato as influenced by repeated waterlogging.

Introduction: Plants respond to water stress with a variety of physiological and biochemical changes, but their response varies among species, varieties and cultivars. Waterlogging in tomato reduces plant growth, degrade chlorophyll and increase concentration of oxidative parameters. Priming can alleviate stress in plants caused by waterlogging enabling plants to be more tolerant to an additional stress in the current or even subsequent generation. The aim of this study was to evaluate tomato genotypes for their sensitivity to waterlogging stress applied during early vegetative growth and at full flowering stage. Materials and methods: The study included two local genotypes, Trebinjski sitni (GB1126) and Zuti (GB1129), and the reference variety Novosadski jabucar (NJ), which is the variety most commonly used in Serbia and Bosnia and Herzegovina. The activity of class III peroxidase (POX), hydrogen peroxide (H2O2) content and malondialdehyde (MDA) content were measured spectrophotometrically, and for quantification of individual phenolic compounds, targeted approach was adopted, using UHPLC/DAD/(-)HESI-MS2 instrument (Dionex UltiMate 3000 UHPLC system with a DAD detector, configured with a triple quadrupole mass spectrometer TSQ Quantum Access Max (Thermo Fisher Scientific, Germany)). Results and discussion: Oxidative parameters (H2O2 and MDA) exhibited an increase in content in leaves of tomato plants that underwent waterlogging stress compared to control plants. Moreover, oxidative parameters showed positive correlation with proteins and phenolics content. The obtained correlations can indicate that one of the response strategies of tomato plants to waterlogging is the increased synthesis of proteins and phenolic compounds. The POX activity was not correlated with other parameters except with the polyphenols. A positive correlation was shown between POX activity and the content of phenolic compounds, indicating their independent roles in the removal of ROS. Changes in the phenolic profiles after the exposure of plants to waterlogging stress are recorded, and these changes were more severe in leaves and fruits of GB1129 and NJ genotypes than in GB1126. Thus, genotype GB1126 is the most efficient in maintaining the phenolic profiles of leaves and fruits, and therefore of the nutritive and organoleptic qualities of fruits following the exposure to waterlogging. Also, genotype GB1126 exhibited the ability to maintain the content of oxidative parameters during waterlogging at certain growth stages, implying certain waterlogging tolerance. Conclusion: Waterlogging triggered stress memory but not at all growth stages. The most pronounced stress memory was obtained in fruit samples in the phase of full fruit maturity on the 1st truss. This study shed light on the defense mechanisms of tomato plants to repeated waterlogging stress from the perspectives of the changes in the composition of major phenolics, and pointed to the 5-O-caffeoylquinic acid and rutin as the chemical markers of the waterlogging stress tolerance in tomato. However, it remains to be determined whether this modulation has a positive or negative effect on the overall plant metabolism. Further investigations are needed to fully elucidate the benefits of waterlogging pretreatment in this context.

Global epidemiology and species/genotype distribution of Cryptosporidium in camels: A systematic review and meta-analysis.

This review analyzed reported data of Cryptosporidium prevalence in camels and the species/genotype distribution. Four databases (PubMed, Web of Science, Scopus, Google Scholar) were screened, and studies published by April 1, 2024, were included. Total estimates and 95% CIs were calculated using a random-effects model. The weighted prevalence of Cryptosporidium spp. in 7372 camels examined from 12 different countries was estimated at 13.8% with a 95% CI of 10.3-18.4%. The sensitivity analysis based on excluding the individual studies did not result in significant statistical changes in the final weighted prevalence. Subgroup prevalence of Cryptosporidium spp. in camels was analyzed by publication year, continent, WHO region, country, camel type, sample size, diagnostic method, age, and gender. A significant publication bias (P < 0.05) was reported in the present study. Limitations encountered in this study encompassed: insufficient study diversity, reliance on single study results, inadequate molecular and serological studies in comparison to microscopic studies, etc., all of which could impact the findings. The study identified eight Cryptosporidium spp. in camels: C. parvum, C. andersoni, C. bovis, C. muris, C. ratti, C. occultus, C. ubiquitum, and C. hominis. The first three species had pooled prevalence rates of 65.5%, 66%, and 19.2%, respectively. Each of the remaining five species was documented using a single dataset/study. Moreover, genotypes IIdA19G1, IIaA15G1R1, If-like-A15G2, IIdA15G1, IIaA15G2R1, IIaA17G2R1, and IIaA18G2R1 (C. parvum), genotype IV (C. ratti), genotype XIIa (C. ubiquitum), and genotype IkA19G1 (C. hominis) have been identified in camels globally. The findings suggest that camels can act as a source of infection for a variety of Cryptosporidium species/genotypes, and can therefore play a key role in disseminating this protozoan to humans and animals.

The Impact of Different MEFV Genotypes on Clinical Phenotype of Patients with Familial Mediterranean Fever: Special Emphasis on Joint Involvement.

Familial Mediterranean Fever (FMF) is the most common monogenic autoinflammatory disease worldwide. In this retrospective cohort study, we aimed to assess the effects of various MEFV genotypes on the clinical characteristics of the patients, with a special focus on the joint involvement. In total, 782 patients with FMF were categorized into 3 groups according to the MEFV mutation; Group 1: Patients homozygous for M694V; Group 2: Patients carrying other pathogenic MEFV variants in exon 10 in homozygous or compound heterozygous states; and Group 3: FMF patients with other variants or without mutations. Clinical and demographic findings were compared between groups. Among the 782 FMF patients, total frequency of arthritis was 237 (30.3%): 207 (26.4%) were acute monoarthritis and 67 (8.5%) were chronic arthritis. Both the frequency of arthritis (acute and/or chronic) (40.4% vs. 24.8% vs. 26.7%; p:0.001) and acute monoarthritis (35.4% vs. 20% vs. 23.7%; p:0.001) were significantly higher in Group 1 than in the other groups. FMF patients with chronic arthritis showed a distinct juvenile idiopathic arthritis (JIA) distribution pattern with a more frequent enthesitis-related arthritis (ERA) subtype (43.2%). HLA-B27 was positive in 24% of the ERA patients.Conclusion: Homozygous M694V mutation is associated with a more frequent and longer acute monoarthritis comparing to other MEFV genotypes. In addition, the risk of chronic arthritis seems not related to the MEFV mutations. However, FMF patients with chronic arthritis show a distinct ILAR JIA distribution pattern with a more frequent ERA and undifferentiated arthritis subtype. What is known: • Homozygous M694V mutation is associated with a more frequent and longer acute monoarthritis What is new: • FMF patients with chronic arthritis show a distinct ILAR JIA distribution pattern with a more frequent ERA subtype • ERA patients with negative HLA-B27 antigen should also be assessed for polyserositis episodes of FMF, especially in countries with high FMF carrier frequency.

Inside Mycobacterium bovis SB0120 spoligotype circulating in Italy: analysis of the most frequent genotypes by whole genome sequencing.

Bovine tuberculosis (bTB) is a chronic inflammatory disease primarily caused by Mycobacterium bovis. The infection affects domestic animals and wildlife, posing a zoonotic risk to humans. To understand the dynamics of transmission and genetic diversity in Italy's M. bovis population, we conducted whole-genome sequencing (WGS) analysis on two prevalent genotypes, belonging to Spoligotype SB0120, identified in different geographical and temporal contexts. By comparing these genomes with international M. bovis isolates, we identified a distinct clade within the lineage La1.2, encompassing the Italian SB0120 isolates, indicating a genomic segregation of Italian M. bovis from other European isolates. Within Italy, a significant level of genetic variability emerged across regions, while isolates within epidemiologically linked outbreaks exhibited minimal genetic diversity. Additionally, isolates derived from cattle and wild boars within a tuberculosis hotspot in Central Italy and from cattle and black pigs in Sicily formed unified clonal clusters. This indicates the presence of persistent strains circulating in the examined regions. The genetic diversity within herds was limited, as specific clones endured over time within certain herds. This research enhances our comprehension of the epidemiology and transmission patterns of bTB in Italy, thereby aiding the development of precise control strategies and disease management. Using WGS and implementing standardized protocols and databases will be pivotal in combating bTB and promoting One-Health approaches to address this noteworthy public health concern.

Mixed-Genotype HCV Direct Acting Antiviral Outcomes: A CANUHC Analysis.

The prevalence of mixed hepatitis C virus (HCV) genotype infection in a representative Canadian HCV cohort is reported and virological response with direct acting antiviral (DAA) treatment was evaluated. 3272 HCV-positive participants were enrolled, of which 2945 (90.0%) initiated DAA therapy. 0.8% were identified with mixed genotype infection. Overall sustained virological response (SVR) was 99.1% and did not differ based on mixed genotype status. Any historical disadvantage to achieving cure with HCV treatment in mixed genotype infection has been overcome by current DAA regimens.

Epidemiological distribution of high-risk human papillomavirus genotypes and associated factors among patients with esophageal carcinoma at Bugando medical center in Mwanza, Tanzania.

BACKGROUND: Esophageal carcinoma is a growing concern in regions that have a high incidence of human papillomavirus (HPV) infection such as East Africa. HPV, particularly the high-risk genotypes, is increasingly recognized as a risk factor for esophageal carcinoma. We set out to investigate the prevalence and associated factors of high-risk HPV in formalin-fixed paraffin-embedded (FFPE) tissue blocks with esophageal carcinoma at Bugando Medical Center, a tertiary referral hospital in Mwanza, Tanzania, East Africa. METHODS: A total of 118 esophageal carcinoma FFPE tissue blocks, collected from January 2021 to December 2022, were analyzed. Genomic DNA was extracted from these tissues, and multiplex polymerase chain reaction (PCR) was performed to detect HPV using degenerate primers for the L1 region and type-specific primers for detecting HPV16, HPV18, and other high-risk HPV genotypes. Data were collected using questionnaires and factors associated with high-risk HPV genotypes were analyzed using STATA version 15 software. RESULTS: Of the 118 patients' samples investigated, the mean age was 58.3 ± 13.4 years with a range of 29-88 years. The majority of the tissue blocks were from male patients 81/118 (68.7%), and most of them were from patients residing in Mwanza region 44/118 (37.3%). Esophageal Squamous Cell Carcinoma (ESCC) was the predominant histological type 107/118 (91.0%). Almost half of the tissue blocks 63/118 (53.3%) tested positive for high-risk HPV. Among these, HPV genotype 16 (HPV16) was the most common 41/63 (65.1%), followed by HPV genotype 18 (HPV18) 15/63 (23.8%), and the rest were other high-risk HPV genotypes detected by the degenerate primers 7/63 (11.1%). The factors associated with high-risk HPV genotypes were cigarette smoking (p-value < 0.001) and alcohol consumption (p-value < 0.001). CONCLUSION: A substantial number of esophageal carcinomas from Bugando Medical Center in Tanzania tested positive for HPV, with HPV genotype 16 being the most prevalent. This study also revealed a significant association between HPV status and cigarette smoking and alcohol consumption. These findings provide important insights into the role of high-risk HPV in esophageal carcinoma in this region.

High-risk human papillomavirus infection and cervical cytopathology: relationship with cervical nitric oxide levels.

BACKGROUND: Nitric oxide (NO) may contribute to the persistence of high-risk human papillomavirus (hrHPV) infection, which has been linked to the development of premalignant lesions and cervical cancer. Our study aimed to examine the relationship between cervical NO metabolite (NOx) levels, hrHPV infection, and cytopathological findings. Additionally, we assessed cervical NOx levels as a biomarker for predicting hrHPV infection and epithelial atypia. METHODS: The study involved 74 women who attended the Gynecology and Obstetrics outpatient clinics at Cairo University Hospitals between November 2021 and August 2022. Cervical samples were subjected to Pap testing, assessment of NOx levels by the Griess method, and detection of hrHPV DNA by real-time polymerase chain reaction. RESULTS: High-risk HPV was detected in 37.8% of women. EA was found in 17.1% of cases, with a higher percentage among hrHPV-positive than negative cases (35.7% vs. 4.3%, p = 0.001). The most prevalent hrHPV genotype was HPV 16 (89.3%). The cervical NOx level in hrHPV-positive cases was significantly higher (37.4 µmol/mL, IQR: 34.5-45.8) compared to negative cases (2.3 µmol/mL, IQR: 1.2-9.8) (p = < 0.001). Patients with high-grade atypia showed significantly higher NOx levels (38.0 µmol/mL, IQR: 24.6-94.7) in comparison to NILM and low-grade atypia cases (5.0 µmol/mL, IQR: 1.6-33.3 and 34.5 µmol/mL, IQR: 11.7-61.7, respectively) (p = 0.006). Although the NOx levels among hrHPV-positive cases with low-grade atypia (40.4 µmol/mL, IQR: 33.3‒61.8) were higher than those with NILM (36.2 µmol/mL, IQR: 35.7‒44.0) and high-grade atypia (38.0 µmol/mL, IQR: 24.6‒94.7), the difference was not significant (p = 0.771). ROC curve analysis indicated that the cervical NOx cut-off values of > 23.61 µmol/mL and > 11.35 µmol/mL exhibited good diagnostic accuracy for the prediction of hrHPV infection and EA, respectively. CONCLUSIONS: The high prevalence of hrHPV infection, particularly HPV 16, in our hospital warrants targeted treatment and comprehensive screening. Elevated cervical NOx levels are associated with hrHPV infection and high-grade atypia, suggesting their potential use as biomarkers for predicting the presence of hrHPV and abnormal cytological changes.

Genetic variations of Toll-like receptor 4 gene in exon 2 of South African Dorper sheep.

Objective: The study was conducted to identify the sequence variation of Toll-like receptor 4 (TLR4) in exon 2 of South African Dorper sheep. Materials and Methods: Blood samples were collected from fifty (n = 50) South African Dorper sheep aged between 3 and 4 years. The Deoxyribonucleic acid (DNA) was extracted, amplified, and sequenced for the TLR4 gene. DNA sequencing was used to identify the sequence variations of the TLR4 gene in South African Dorper sheep. Results: The results showed that one synonymous single nucleotide polymorphism (SNP) of the TLR4 gene in exon 2 position T2249C was identified. Two genotypes (TT and TC) were discovered from the identified SNP. The dominant genotype was TT (0.60) over TC (0.40), with the dominant allele T (0.80) over C (0.20). The results also indicated that the used population was in the Hady-Weinberg Equilibrium. Polymorphism genetic analysis findings suggest that the identified sequence variation of TLR4 in exon 2 of South African Dorper sheep was moderate polymorphism. Conclusion: TLR4 gene at exon 2 of South African Dorper sheep had the SNP (T>C) at position 2249 bp with two genotypes (TT and TC).

Unraveling genetic, compositional, and organoleptic traits of elephant garlic of different geographical origins.

The ancient native variety of elephant garlic, known as "Aglione della Valdichiana" and cultivated in the Valdichiana area of Tuscany, Italy, has gained recent recognition in the National Catalog of Local Varieties. The renewed interest in traditional products has led to a focus on identifying local varieties of elephant garlic, driven by their distinctive organoleptic and nutritional characteristics. However, other types of elephant garlic nowadays available on the market appear similar, but challenges exist in discerning their origin and composition. This study focused on characterizing elephant garlic from Lazio, Italy, and the Val di Chiana region through genetic, chemical, and aromatic analyses to understand genetic and geographic influences. ISSR markers differentiated elephant garlic from common varieties and highlighted regional genetic diversity. Chemical analysis revealed higher polyphenol content and antioxidant activity in elephant garlic compared to common garlic. Moreover, analysis highlights the variability in the concentrations of sulfur-containing compounds between common and elephant garlic. Aromatic and sensory assessments underscored distinctions between garlic types and regions, emphasizing the significant impact of geographic origin and genetic background on metabolite profiles in Allium genotypes.

Global distribution and definitive host range of Echinococcus species and genotypes: A systematic review.

Echinococcus species (spp.) are regarded as neglected cestodes causing several potential zoonoses of global public health. This systematic review critically appraises the worldwide distribution of Echinococcus spp. and genotypes (Echinococcus spp.: recognized species in the genus; genotypes: variants identified within E. granulosus sensu lato.) in definitive hosts. We analyzed 82 studies from major databases, comprising 24 individual host species, including canids, felids, and a hyenid species. Canids, particularly dogs, were the most studied group among the host species, with E. granulosus sensu stricto (G1-G3) being the most frequently reported. E. granulosus s.s. was distributed across five major continents, while other Echinococcus spp. and genotypes exhibited an uneven continental distribution. The highest overlap of species existed among Asia, Europe, and Africa. Among the reported host species, 4.2 % were endangered (e.g. Lycaon pictus), 12.5 % species were vulnerable (e.g. Panthera leo, Panthera pardus, and Acinonyx jubatus), and 4.2 % were near threatened (e.g. Speothos venaticus). Overall, our review highlights the significance of canids, particularly dogs, as the core focus of scientific investigations, with E. granulosus s.s. being the most widely distributed species across five major continents, emphasizing the urgent need for continued research and public health efforts.

A new evaluation of the rearranged non-coding control region of JC virus in patients with colorectal cancer.

BACKGROUND: Several studies have reported the presence of JC virus (JCV) in human tumors, The association of JCV and CRC remains controversial. This study aimed to evaluate the rearranged NCCR region of the detected JCV DNA in CRC patients' tissue samples. METHODS: In this case-control study, tumor tissues (n = 60), adjacent normal tissues (n = 60), and urine samples (n = 60) of the CRC patients were collected. The nested PCR was employed to detect the VP1 and NCCR regions of the JCV genome. The positive JCV PCR products were sequenced and a phylogenetic tree was constructed to determine the JCV genotypes. After extracting RNA and preparing cDNA, the expression of JCV LTAg was examined in 60 tumor tissues and 60 adjacent normal tissues. The analysis of JCV LTAg expression was performed using GraphPad Prism software version 8. RESULTS: The analysis reveals that JCV DNA was detected in 35/60 (58.3%) tumor tissues, while 36/60 (60.0%) of adjacent normal tissues (p = 0.85). JCV DNA was detected in 42/60 (70.0%) urine samples when compared to 35/60 (58.3%) tumor tissues of CRC patients and was not found significant (P = 0.25). The phylogenetic tree analysis showed the dominant JCV genotype 3, followed by genotype 2D was distributed in tumor tissue, normal tissue, and urine samples of the CRC patients. Analysis of randomly selected NCCR sequences from JCV regions in tumor tissue samples revealed the presence of rearranged NCCR blocks of different lengths.: 431 bp, 292 bp, 449 bp, and 356 bp. These rearranged NCCR blocks differ from the rearranged NCCR blocks described in PML-type Mad-1, Mad-4, Mad-7, and Mad-8 prototypes. The expression of JCV LTAg was significantly different in tumor tissue compared to normal tissue, with a p-value of less than 0.002. CONCLUSION: A significant proportion of 35%> of the tumor tissue and urine samples of the CRC patients was found to be positive for JCV DNA (P = 0.25). The parallel analysis of tumor and urine samples for JCV DNA further supports the potential for non-invasive screening tools. This study provides new insights into Rearranged NCCR variant isolates from patients with CRC. The significant difference in JCV LTAg expression between tumor and normal tissue indicates a latent JCV status potentially leading to cancer development.

How to customize common data models for rare diseases: an OMOP-based implementation and lessons learned.

BACKGROUND: Given the geographical sparsity of Rare Diseases (RDs), assembling a cohort is often a challenging task. Common data models (CDM) can harmonize disparate sources of data that can be the basis of decision support systems and artificial intelligence-based studies, leading to new insights in the field. This work is sought to support the design of large-scale multi-center studies for rare diseases. METHODS: In an interdisciplinary group, we derived a list of elements of RDs in three medical domains (endocrinology, gastroenterology, and pneumonology) according to specialist knowledge and clinical guidelines in an iterative process. We then defined a RDs data structure that matched all our data elements and built Extract, Transform, Load (ETL) processes to transfer the structure to a joint CDM. To ensure interoperability of our developed CDM and its subsequent usage for further RDs domains, we ultimately mapped it to Observational Medical Outcomes Partnership (OMOP) CDM. We then included a fourth domain, hematology, as a proof-of-concept and mapped an acute myeloid leukemia (AML) dataset to the developed CDM. RESULTS: We have developed an OMOP-based rare diseases common data model (RD-CDM) using data elements from the three domains (endocrinology, gastroenterology, and pneumonology) and tested the CDM using data from the hematology domain. The total study cohort included 61,697 patients. After aligning our modules with those of Medical Informatics Initiative (MII) Core Dataset (CDS) modules, we leveraged its ETL process. This facilitated the seamless transfer of demographic information, diagnoses, procedures, laboratory results, and medication modules from our RD-CDM to the OMOP. For the phenotypes and genotypes, we developed a second ETL process. We finally derived lessons learned for customizing our RD-CDM for different RDs. DISCUSSION: This work can serve as a blueprint for other domains as its modularized structure could be extended towards novel data types. An interdisciplinary group of stakeholders that are actively supporting the project's progress is necessary to reach a comprehensive CDM. CONCLUSION: The customized data structure related to our RD-CDM can be used to perform multi-center studies to test data-driven hypotheses on a larger scale and take advantage of the analytical tools offered by the OHDSI community.

Association Between FADS1 Gene Polymorphism (rs174549) and Chronic Periodontitis: A Cross-Sectional Study.

Introduction FADS1 (fatty acid desaturase 1) gene polymorphism results in more susceptibility to certain metabolic diseases and chronic inflammatory diseases like periodontitis. This study aims to analyze the association between FADS1 gene polymorphism and various stages of periodontitis. Materials and methods One hundred subjects included in the study were categorized into two groups: group A (n = 50) had healthy periodontium, and group B (n = 50) had ≥stage II periodontitis. They were graded based on the clinical parameters of probing pocket depth (PPD), clinical attachment level (CAL), and bleeding on probing (BOP). Five milliliters of venous blood were collected, and DNA isolation was done. Genomic DNA was extracted. The DNA was then subjected to amplification with the help of specific primers flanking the Providencia stuartii I (PstI) polymorphic site of the FADS1 gene. A chi-square test aimed to examine the genotype and allele frequency distributions in both groups; p < 0.05 was considered statistically significant. Results The difference in genotype frequency of FADS1 polymorphism was statistically insignificant (p = 0.91). Our study revealed no significant difference (AA vs. AG+GG) between the periodontitis and control groups between homozygous and heterozygous variant genotypes with a p-value of 0.7764. The frequency of AG (28% vs. 30%) and GG (62% vs. 58%) genotypes showed no significant difference between the periodontitis group and healthy control subjects. No significant difference was seen in the G allele (77% vs. 73%) and A allele (23% vs. 27%) between the periodontitis and control groups. Conclusion The study concluded that FADS1 receptor polymorphism is not associated with periodontitis in the study population.

Identifying selection signatures for immune response and resilience to Aleutian disease in mink using genotype data.

Aleutian disease (AD) brings tremendous financial losses to the mink industry. Selecting AD-resilient mink has been conducted to control AD. Such selections could have altered the patterns of genetic variation responding to selection pressures. This study aimed to identify selection signatures for immune response (IRE) and resilience to AD. A total of 1,411 mink from an AD-positive facility were used. For IRE, 264 animals were categorized according to the combined results of enzyme-linked immunosorbent assay (ELISA) and counterimmunoelectrophoresis (CIEP). For resilience, two grouping methods were used: 1) general resilience performance (GRP, n = 30) was evaluated based on the feed conversion ratio, Kleiber ratio, and pelt quality; and 2) female reproductive performance (FRP, n = 36) was measured based on the number of kits alive 24 h after birth. Detection methods were the pairwise fixation index, nucleotide diversity, and cross-population extended haplotype homozygosity. A total of 619, 569, and 526 SNPs were identified as candidates for IRE, GRP, and FRP, respectively. The annotated genes were involved in immune system process, growth, reproduction, and pigmentation. Two olfactory-related Gene Ontology (GO) terms were significant (q < 0.05) for all traits, suggesting the impact of AD on the sense of smell of infected mink. Differences in detected genes and GO terms among different color types for IRE indicated variations in immune response to AD among color types. The mitogen-activated protein kinase (MAPK) signaling pathway was significant (q < 0.05) for FRP, suggesting that AD may disrupt MAPK signaling and affect FRP. The findings of this research contribute to our knowledge of the genomic architecture and biological mechanisms underlying AD resilience in mink.

Characterization of zoonotic hepatitis E virus in domestic pigs and wild boar in Vietnam: Implications for public health.

Vietnam's unprecedented demand for meat from livestock, including pigs and farmed wildlife, underscores the importance of understanding zoonotic reservoirs for hepatitis E virus (HEV). This study aimed to identify and characterize circulating zoonotic HEV in domestic pigs and wild boar to understand genotype frequencies, transmission dynamics, and associated human health burdens. Rectal swabs, feces, and liver samples from 415 pigs and 102 wild boars were collected across various farms and slaughterhouses in central and southern Vietnam and screened for HEV RNA using nested PCR. HEV RNA-positive samples underwent sanger sequencing and genotyping. Overall, 10% (n = 54/517) of samples were HEV RNA-positive, with wild boars exhibiting the highest HEV positivity rate at 25%, followed by domestic pigs at 7%. Southern Vietnam showed a higher HEV RNA positivity rate (20%) compared to central Vietnam (7%). Notably, rectal swabs demonstrated the highest positivity rate (15%), followed by feces (8%) and liver (4%). HEV-3a was the predominant genotype at 85%, followed by HEV-4b at 9% and HEV-3f at 6%. While HEV-3a was distributed across both central and southern Vietnam, HEV-3f was exclusively detected in central Vietnam, and HEV-4b was identified in wild boar in southern Vietnam. These findings underscore the substantial prevalence of HEV in wild boars, emphasizing their potential as crucial zoonotic reservoirs alongside domestic pigs. Further investigations involving occupationally exposed individuals in high-prevalence areas are warranted to evaluate the human health impact of zoonotic hepatitis E and inform preventive measures. Regular epidemiological studies are imperative for assessing the prevalence and transmission of zoonotic HEV infections among common reservoirs, thereby aiding in the prevention of spillover events within the community.

Molecular Characterization of Enteric Viruses Causing Acute Gastroenteritis among Children under 5 Years Old in Distrito Central, Honduras.

INTRODUCTION: Diarrheal diseases constitute a significant public health problem in terms of mortality and morbidity. In Honduras and around the world, RVs have consistently emerged as the single most important etiologic agent in acute childhood diarrhea. However, other viruses, such as NoVs and HAstVs, have also been shown to be responsible for viral gastroenteritis. Unfortunately, the country has limited information concerning the etiologic role of these viral agents in acute gastroenteritis. This study investigated the frequency, genotypes, and epidemiological characteristics of RV-A, NoVs, and HAstVs among children under 5 years old in Distrito Central, Honduras. METHODS: Stool samples and their corresponding epidemiological data were collected from children with acute gastroenteritis in three healthcare centers in Distrito Central. All samples were screened by immunoassays for RV-A and HAstVs. RV-A-positive samples were molecularly characterized by RT-PCR and genotyping assays. RT-PCR was also applied to confirm HAstVs positivity and to detect NoVs, followed by nucleotide sequencing to assign their genotypes. RESULTS: Our results show that at least one viral agent was detected in 31% of the children. The frequency of RV-A, NoVs, and HAstVs was 14%, 13%, and 5%, respectively. The most frequent RV-A genotype was G2P[4], occurring in 93% of cases. 92.3% of NoVs-positive samples belonged to genogroup II, with GII.4 and GII.16 being the most common. HAstVs were clustered into three genotypes: HAstV-1, HAstV-2, and HAstV-8. Only one sample showed coinfection with NoVs and HAstVs. CONCLUSION: This comprehensive molecular and epidemiological characterization of enteric viruses demonstrates the vast diversity of these agents and describes for the first time NoVs and HAstVs as causative agents of acute childhood gastroenteritis in Distrito Central, Honduras. This suggests that further in-depth studies of the pediatric population are necessary to develop and implement effective preventive and control measures in the country.

Prevalence of HPV Genotypes among Greek Women in Association with Their Potential to Cause Precancerous Lesions.

The escalating global rates of precancerous lesions associated with human papillomavirus (HPV) types not targeted by current vaccines underscore the need to explore the prevalence of HPV types within the Greek female population and their involvement in precancerous lesion development. In the current study, we enrolled a cohort of 253 women aged 18 to 65 years, residing in Greece, who underwent routine screening in three tertiary care referral hospitals. Each participant completed a demographic questionnaire. An HPV DNA test was administered using the VisionArray® HPV kit (ZytoVision GmbH) to qualitatively detect and genotype 41 clinically relevant HPV genotypes. Of all 253 women examined, 114 (45.1%) tested positive for HPV DNA. The primary type detected was HPV51 (high-risk), present in 21 women (8.3% of the total), followed by HPV54 (low-risk) in 17 women (6.7%); HPV16 (high-risk) ranked third, identified in 14 women (5.5%). Among the HPV-positive women, 65 were positive for high-risk HPV types (57% of HPV-positive women) and were referred for colposcopy and cervical biopsy. These procedures identified 24 women with cervical intraepithelial neoplasia 1 (CIN1) lesions and 2 with cervical intraepithelial neoplasia 2 (CIN2) lesions. The most prevalent HPV type among women with CIN1 lesions was HPV16, found in nine (37.5%) women, while HPV51 ranked second, identified in six (25%) women. Both women with CIN2 lesions tested positive for HPV16, whereas one of them was also tested positive for HPV45. Our study is the first to report the prevalence of HPV51 among HPV-positive women in the Greek female population. This highlights the need for further research to fully understand the potential of HPV types not covered by current vaccines, such as HPV51, to cause high-grade lesions or cervical cancer.