Cherry virus A (CVA) infection appears to be prevalent in cherry plantations worldwide. In this study, the diversity of CVA isolates from 31 cherry samples collected from different orchards around Bohai Bay in northeastern China was analyzed. The complete genome of one of these isolates, ChYT52, was found to be 7,434 nt in length excluding the poly (A) tail. It shares between 79.9–98.7% identity with CVA genome sequences in GenBank, while its RdRp core is more divergent (79.1–90.7% nt identity), likely as a consequence of a recombination event. Phylogenetic analysis of ChYT52 genome with CVA genomes in Genbank resulted in at least 7 major clusters plus additional 5 isolates alone at the end of long branches suggesting the existence of further phylogroups diversity in CVA. The genetic diversity of Chinese CVA isolates from 31 samples and GenBank sequences were analyzed in three genomic regions that correspond to the coat protein, the RNA-dependent RNA polymerase core region, and the movement protein genes. With few exceptions likely representing further recombination impact, the trees various trees are largely congruent, indicating that each region provides valuable phylogenetic information. In all cases, the majority of the Chinese CVA isolates clustering in phylogroup I, together with the X82547 reference sequence from Germany. Statistically significant negative values were obtained for Tajima’s D in the three genes for phylogroup I, suggesting that it may be undergoing a period of expansion. There was considerable haplotype diversity in the individual samples and more than half samples contained genetically diverse haplotypes belonging to different phylogroups. In addition, a number of statistically significant recombination events were detected in CVA genomes or in the partial genomic sequences indicating an important contribution of recombination to CVA evolution. This work provides a foundation for elucidation of the epidemiological characteristics and evolutionary history of CVA populations.

We analyzed virus and viroid communities in five individual trees of two nectarine cultivars with different disease phenotypes using next-generation sequencing technology. Different viral communities were found in different cultivars and individual trees. A total of eight viruses and one viroid in five families were identified in a single tree. To our knowledge, this is the first report showing that the most-frequently identified viral and viroid species co-infect a single individual peach tree, and is also the first report of peach virus D infecting Prunus in China. Combining analyses of genetic variation and sRNA data for co-infecting viruses/viroid in individual trees revealed for the first time that viral synergisms involving a few virus genera in the Betaflexiviridae , Closteroviridae , and Luteoviridae families play a role in determining disease symptoms. Evolutionary analysis of one of the most dominant peach pathogens, peach latent mosaic viroid (PLMVd), shows that the PLMVd sequences recovered from symptomatic and asymptomatic nectarine leaves did not all cluster together, and intra-isolate divergent sequence variants co-infected individual trees. Our study provides insight into the role that mixed viral/viroid communities infecting nectarine play in host symptom development, and will be important in further studies of epidemiological features of host-pathogen interactions.

Background Most immune thrombocytopenia (ITP) is sporadic but a positive family history of ITP in some patients suggests that hereditary forms exist. Because of the rarity of familial ITP families available for study and the heterogeneity of sporadic ITP, family linkage analysis or genome-wide association studies are limited. Objectives Based on one ITP pedigree, we try to identify the predisposing gene in familial or sporadic ITP and reveal the way in which it causes thrombocytopenia. Methods Gene expression profiling analysis and whole-exome sequencing were performed on samples from family members with ITP, sporadic ITP cases and healthy individuals. We also evaluated the influence of potential pathogenic mutation on immune function and megakaryocyte apoptosis. Results Whole-exome sequencing identified a potential pathologic p.G76S heterozygous mutation on the TNFRSF13B gene in familial ITP patients. ITP patients harboring the G76S mutation displayed an upregulated 'cytokine-cytokine receptor interaction' signal, increased serum TNFα, IL-17α, IFNγ and BAFF levels, and enhanced binding capacity of APRIL ligand to B cells. Additionally, Epstein-Barr virus (EBV)-transformed B cells with the G76S mutation could induce human megakaryocyte line (Meg-01) apoptosis significantly. Conclusion p.G76S mutation on the TNFRSF13B gene is responsible for ITP, and is a genetic predisposing factor for familial or sporadic ITP.

Significance and Impact of the Study: In this study, we developed a multiplex reverse transcriptase PCR (mRT-PCR) assay for simultaneously detecting three viruses that infect peach: peach-associated luteovirus (PaLV), peach virus D (PeVD) and nectarine stem-pitting-associated virus (NSPaV). This assay is simple, easy to perform, reliable and cost-effective, and can thus be applied for large-scale surveys of PaLV, PeVD and NSPaV. AbstractPeach is a major crop in China, and like any other stone fruit, virus and viruslike diseases can reduce the yield and quality of the fruit. Herein, we developed a multiplex RT-PCR (mRT-PCR) assay for simultaneously detecting three viruses known to infect peach: peach-associated luteovirus (PaLV), peach virus D (PeVD) and nectarine stem-pitting-associated virus (NSPaV). Plant nad5 mRNA was used as the internal control. Field samples that were co-infected with PaLV, PeVD and NSPaV were used; we identified three primer pairs to be the most specific for detecting these viruses, followed by determining the ideal concentration of each primer pair and optimizing the annealing temperature for mRT-PCR. We also assessed the detection limit using serial dilutions of RNA and cDNA. The newly developed mRT-PCR assay could simultaneously detect PaLV, PeVD and NSPaV. To validate the reliability of mRT-PCR for virus detection, mRT-PCR was used to detect viruses in the leaves of 21 peach plants collected in Liaoning Province, China. The obtained results revealed the presence of single and co-infections. To conclude, the mRT-PCR assay developed herein is sensitive, reliable and economical, and we believe that it can thus be used for large-scale surveys of PaLV, PeVD and NSPaV.Letters in Applied Microbiology ISSN 0266-8254

Here, we report the complete genome sequence of a divergent cherry virus A (CVA) isolate (ChYT56) from Prunus avium in China. The genome nucleotide sequence has low identity (80.7%) with a CVA from P. avium (GenBank accession number FN691959) and high identity (97%) with a CVA from P. armeniaca (GenBank accession number LC125634).

Backgroud: Diffuse large B-cell lymphomas (DLBCLs) are featured as phenotypically and genetically heterogeneous. Ferroptosis is a newly discovered regulated cell death pathway that plays a crucial role in the occurrence and progression of tumors. We aim to identify a ferroptosis-related gene (FRG) prognostic signature for DLBCLs by systematic analysis of transcriptional profiles. Methods: This study retrospectively analysed the transcriptome profiles and clinical parameters of 604 DLBCL patients from 3 public datasets. A series of bioinformatic approaches including univariate and multivariate Cox regression analysis, function analysis, immune infiltration analysis, differential expression analysis, ROC curve analysis, Kaplan–Meier survival curve and the least absolute shrinkage and selection operator (LASSO) method by the corresponding R packages in R software were combined to explored the heterogenicity of FRG based clusters and to built prognostic model. Immunohistochemistry was used to exam the protein expression of six FRGs in different type of DLBCL.Results: We first identified 19 FRGs with potential prognostic values and classfied the patients into two subgroups (named cluster 1 and cluster 2), Results showed that there were different patterns of immune cell infiltration among patients in the two clusters. Furthermore, the LASSO was used to generated a six genes (GCLC, LPCAT3, NFE2L2, ABCC1, SLC1A5, and GOT1) risk signature which constructed a risk score formula and prognostic model for the overall survival (OS) of DLBCL patients. Kaplan–Meier survival analysis proved that poorer OS was exhibited in higher risk patients stratified by the prognostic model in both the training cohort and test cohort. In addtion, we constructed nomograms to predict the OS of DLBCL patients. Both the decision curve(DCA) and the calibration plots showed that the nomogram had good predictive performance. Finally, the validation by immunohistochemistry indicated the GCLC, LPCAT3, NFE2L2, SLC1A5, and GOT1 were high expressed in DLBCL with various prognostic adverse molecular factor. Conclusion: In sum, we built a new FRG-based prognostic model which will help improve diagnosis and treatment for DLBCL patients.