Exploring virus presence in field-collected potato leaf samples using RNA sequencing.

BACKGROUND: The quick and accurate identification of viruses is essential for plant disease management. Next-generation sequencing (NGS) technology may allow the discovery, detection, and identification of plant pathogens. This study adopted RNA-sequencing (RNA-Seq) technology to explore the viruses in three potato plants (S3, S4, and S6) growing under field conditions. RESULTS: Potato-known infecting viruses, such as alfalfa mosaic virus (AMV), potato leafroll virus (PLRV), and potato virus Y (PVY), were identified using bioinformatics programs and validated using RT-PCR. The presence of these potato viruses was also confirmed by visual inspection of host symptoms. In addition, the nearly complete genome of PLRV and the complete or partial genome sequence of multipartite virus segments have been identified. Besides the three major potato viruses that BLASTn analysis revealed were present in our samples, BLASTx analysis revealed some reads are derived from other potato viruses, such as potato virus V (PVV), Andean potato latent virus (APLV), and tomato chlorosis virus (ToCV), which are not frequently reported in potato field screenings in Egypt. Other microbial agents, such as bacteria and fungi, were also identified in the examined sample sequences. Some mycovirus sequences derived from ourmia-like viruses and Alternaria alternata chrysovirus were also identified in sample S4, confirming the complexity of the potato microbiome under field conditions. CONCLUSION: NGS quickly and accurately identifies potato plant viruses under field conditions. Implementing this technology on a larger scale is recommended to explore potato fields and imported plants, where symptoms may be absent, unspecific, or only triggered under certain conditions.

TNF-α versus IL-6 Genes Expression levels in Active Rheumatoid Arthritis: Clinical and Laboratory Determinants.

This study intended to compare the expression levels of tumor necrosis factor-alpha (TNF-α) and interleukin 6 (IL-6) genes in active rheumatoid arthritis (RA) patients who were receiving conventional synthetic disease-modifying drugs (csDMARDs) and to find the clinical and laboratory determinants affecting TNF-α and IL-6 genes expression levels among active RA patients. This was a cross sectional study that included 108 active RA patients who were receiving csDMARDs. A detailed history was reviewed for all patients in addition to a complete physical examination and assessment of the 28-joint disease activity score (DAS28). Some laboratory measures were recorded as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and serum rheumatoid factor (RF). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure expression levels of TNF- α and IL-6 genes. In active RA patients, TNF-α and IL-6 genes expression levels were significantly correlated to each other (p<0.001, r=0.788). Also, both had positive correlations with the age and DAS28 among RA patients (p<0.001). IL-6 and TNF-α expression levels were significantly higher in RA patients with high DAS28 scores (p<0.001). Most RA patients (81.5%) had relatively higher IL-6 gene expression levels than TNF-α. RA patients with relatively high IL-6 expression levels were younger in age and had shorter disease duration and less DAS28 than RA patients with relatively high TNF-α gene expression levels. In addition, they had higher CRP and RF levels. Young age was detected as a significant predictor for relatively higher IL-6 gene expression levels than TNF-α. In conclusion, most active RA patients had higher IL-6 gene expression levels than TNF-α. Young age could be considered a significant predictor for relatively high IL-6 gene expression levels among active RA patients.

Plasma Wnt7b protein in rheumatoid arthritis: Detection of interstitial lung disease.

OBJECTIVE: To determine the plasma level of Wingless-related integration site 7b (Wnt7b) protein in rheumatoid arthritis (RA) patients (with and without interstitial lung disease (ILD)) and in idiopathic pulmonary fibrosis (IPF) patients and its relationship with RA disease activity and/or severity of pulmonary fibrosis. To assess the validity of plasma Wnt7b for the detection of ILD among RA patients. METHOD: This case-control study included 128 subjects (32 RA-ILD, 32 RA, 32 IPF, and 32 healthy controls). RA and RA-ILD Patients were evaluated for disease activity by DAS28 and disease activity grades were recorded according to DAS28 grades. Laboratory parameters as Erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), Rheumatoid Factor (RF), Anti-citrullinated peptide (Anti-CCP) were recorded. Plasma Wnt7b levels were measured by ELISA. Diagnosis of pulmonary fibrosis (for RA-ILD and IPF patients) was done by high resolution computed tomography (HRCT) and its severity was assessed mainly by pulmonary function test using forced vital capacity (FVC) grading. RESULTS: Comparison of Wnt7b plasma levels showed a significant difference between the studied groups with the P-value < 0.018 (RA-ILD had the highest levels). Post hoc analysis revealed a significant difference in Wnt7b plasma levels between RA-ILD and IPF groups (P = 0.008). Also, RA-ILD and control groups had a significant difference (P = 0.039). However, there was a non-significant relationship between Wnt7b plasma levels and RA disease activity as well as the severity of pulmonary fibrosis. ROC curve analysis for the plasma Wnt7b levels revealed that a level  ≥285.1 pg/ml had a sensitivity of 87.5% and a specificity of 43.8% for the detection of ILD in RA patients with positive likelihood ratio of 1.56 and negative likelihood ratio of 0.29. CONCLUSION: RA-ILD patients had significantly higher plasma Wnt7b levels than the controls and IPF patients. These data suggest that the Wnt7b secretion is augmented by the concomitant presence of RA with pulmonary fibrosis. In addition, plasma Wnt7b may be used as a highly sensitive test for the detection of immunologically induced fibrotic changes in lung tissue among RA patients.

Damage accrual in Behçet disease: Behçet's Syndrome Overall Damage Index (BODI) versus Behçet's Disease Damage Index (BDI).

OBJECTIVES: To assess the validity of Behçet's Syndrome Overall Damage Index (BODI) and Behçet's Disease Damage Index (BDI) as tools for the detection of damage accrual in Behçet's patients compared to Vasculitis Damage Index (VDI). Also, to evaluate the correlation and the interclass correlation among the 3 indices to find out their consistency. METHOD: A prospective cohort study was carried out on 102 adult Behçet's disease (BD) patients who were diagnosed according to the International Study Group criteria for BD. Disease severity and organ damage were assessed for each patient by VDI, BDI and BODI at baseline and 1-year follow-up visits. Damage accrual for each index was defined when there was an increase of at least 1 point (∆ ≥ 1) among the baseline and the follow-up visits. RESULTS: Correlations among the 3 indices were significant, with (r = 0.835, P < 0.001) between VDI and BODI, (r = 0.835, P < 0.001) between VDI and BDI, and (r = 0.844, P < 0.001) between BODI and BDI scores. A highly significant positive correlation existed between the 3 indices and age and disease duration. In contrast, the correlation with the BD Current Activity Form was non-significant, which indicates good discriminative validity of the 3 indices. Neuropsychiatric and ocular systems showed a strong interclass correlation among the 3 indices. Regarding detecting damage accrual, BDI was more sensitive than BODI and showed more agreement with VDI. CONCLUSION: BD damage indices, VDI, BODI and BDI, had good convergent and discriminative validity for the assessment of BD damage. BDI had more sensitivity than BODI to the detection of damage accrual.

Validity of systemic lupus erythematosus disease activity score (SLE-DAS) for definition of lupus low disease activity state (LLDAS).

INTRODUCTION: SLE disease activity score (SLE-DAS) is a novel, rapid, continuous and comprehensive score that overcomes the drawbacks of SLEDAI-2 K. Low lupus disease activity state (LLDAS) has been targeted as an endpoint in many clinical trials and as a favourable outcome in clinical practice. Therefore, our objective in the current study is to evaluate the validity of SLE-DAS for defining LLDAS as an objective in the treat-to-target strategy. METHODS: A cross-sectional study was carried out on 117 SLE patients who were diagnosed according to Systemic Lupus International Collaborating Clinics (SLICC) classification criteria for SLE. Patients were evaluated for disease activity by both SLEDAI-2 K and SLE-DAS. Additionally, patients were divided according to the SLEDAI-2 K-derived LLDAS definition into two groups: low disease activity (LDA) group and high disease activity (HDA) group. The validity of SLE-DAS for the definition of LLDAS was evaluated in comparison to SLEDAI-2 K. RESULTS: SLE-DAS shows highly significant positive correlation (r = 0.743, p < 0.001) with SLEDAI-2 K. The ROC curve revealed that SLE-DAS is valid for the assessment of activity with the best detection of LLDAS was at 6.62 with 95.5% sensitivity, 79.3% specificity and 89.6% accuracy. Moreover, it had a good agreement with the SLEDAI-2 K-derived definition of LLDAS (k = 0.765, p < 0.001). CONCLUSION: SLE-DAS is a valid score for the definition of LLDAS which can be used in the clinical practice as a simple and precise standalone criterion. Key Points • Correlation between SLEDAI-2K and SLE-DAS revealed a high significance. • Identify SLE-DAS cut-off 6.62 for the definition of LLDAS. • There is a good agreement between SLEDAI-2K-derived definition of LLDAS and SLE-DAS definition.