Differential DNA methylation profiles of human B lymphocytes and Epstein-Barr virus-immortalized B lymphocytes

Objective： This study aimed to comprehensively assess Epstein-Barr virus（EBV）-induced methylation alterations of B cell across whole genome.Methods： We compared DNA methylation patterns of primary B cells and corresponding lymphoblastoid cell lines（LCLs） from eight participants. The genome-wide DNA methylation profiles were compared at over 850,000 genome-wide methylation sites.Results： DNA methylation analysis revealed 87,732 differentially methylated Cp G sites, representing approximately 12.41% of all sites in LCLs compared to primary B cells. The hypermethylated and hypomethylated Cp G sites were about 22.75% or 77.25%, respectively. Only 0.8% of hypomethylated sites and 4.5% of hypermethylated sites were located in Cp G islands, whereas 8.0% of hypomethylated sites and 16.3% of hypermethylated sites were located in shore（N_shore and S_shore）. Using principal component analysis of the DNA methylation profiles, primary B cells and LCLs could be accurately predicted. Gene Ontology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG） analysis of differently methylated genes revealed that most of the top GO biological processes were related to cell activation and immune response, and some top enrichment pathways were related with activation and malignant transformation of human B cells.Conclusions： Our study demonstrated genome-wide DNA methylation variations between primary B cells and corresponding LCLs, which might yield new insight on the methylation mechanism of EBV-induced immortalization.

Studies on the phenotypic and genotypic characteristics of SA14 wild Japanese encephalitis virus and its attenuated viruses

The aim of this study was to explore the molecular basis for the attenuation of the Japanese encephalitis vires （JEV） vaccine strain SA14-14-2. The virulence of SA14 wild Japanese encephalitis virus （JEV） and its several attenuated viruses was tested by intracerebral （i. c. ） or intraperitonial （i. p. ） inoculation of 10-12 g mice. The stability of neumattenuation was tested by one passage in suckling mouse brain. The E protein genes of those viruses were amplified by PCR, sequenced and compared. Three attenuated virus strains, SA14-14-2 vaccine virus, SA14-9-7 and SA14-5-3, did not exhibit lethal infections by i.c. or i.p. inoculation of 10-12 g mice and revert to the virulence. The other virus strain, SA14-12- 1-7, showed no neuminvasiveness by i.p. inoculation but residual neurovimlence by i.c. inoculation and reverted to high virulence after one brain passage. Comparison of the E protein gene sequences of the five virus strains indicated that there were differences of twelve nucleotides and eight amino acids between the parent strain SA14 and vaccine strain SA14-14-2, of which six amino acids （E-107, E-176, E-439, E-138, E-279, E-315） exhibited changes common to those of SA14-9-7 and SA14-5-3, three substitutions common to SA14-12-1-7. Two amino acid substitutions at the sites E177 （T→A） and E264 （Q→H） are unique to the SA14-14-2 vaccine virus. The results suggest that the mutations of E-107 （Leu→Phe）, E- 176 （Ile→Val）, and E-439 （Lys→Arg） may contribute for the attenuation of neuminvasiveness and partially for the attenuation of neumvirulence, the mutations of E-138, E-279, E-315 may not only critical to the neumattenuation but also to its stability.

The stability of E protein gene of the Japanese encephalitis live attenuated vaccine virus SA_(14)-14-2

The purpose of this study was to understand the stability and possibility of back mutation of Japanese encephalitis （JE） attenuated vaccine virus strain SA14-14-2 HKs on molecular level. The E genes of the SA14-14-2 HKs vaccine virus and its PHK cells passaged virus （SA14-14-2 HK17 ）, its mouse brain passaged virus （SA14-14-2 SM1 ） were sequenced and compared with the E gene of parental SAI4 virus. The total RNA was extracted from infected Vero cells and amplified by RT-PCR. The RT-PCR products were purified and cloned into T-vector. Positive clones were screened, identified and sequenced. There were twelve nucleotides and eight amino acids substitutions between SA14 parent virus and SA14-34-2 PHKs vaccine virus. The SA14-14-2 PHK17 virus showed two additional mutations （E-331 and E-398） which were not back mutations. Although five additional mutations were found in SA14-34-2 SMt virus, only one （E-307） was back mutation. Genetic characteristics of the attenuated vaccine virus SA14- 34-2 were stable when it was passaged 37 times on PHK cells or one time in mouse brains.

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens

Objective Unbiased next generation sequencing（NGS） is susceptible to interference from host or environmental sequences. Consequently, background depletion and virome enrichment techniques are usually needed for clinical samples where viral load is much lower than background sequences. Methods A viral Sequence Independent Targeted Amplification（VSITA） approach using a set of non-ribosomal and virus-enriched octamers（V8） was developed and compared with traditionally used random hexamers（N6）. Forty-five archived clinical samples of different types were used in parallel to compare the V8 and N6 enrichment performance of viral sequences and removal performance of ribosomal sequences in the step of reverse transcription followed by quantitative PCR（qP CR）. Ten sera samples from patients with fever of unknown origin and 10 feces samples from patients with diarrhea of unknown origin were used in comparison of V8 and N6 enrichment performance following NGS analysis. Results A minimum 30 hexamers matching to viral reference sequences（sense and antisense） were selected from a dataset of random 4,096（4~6） hexamers（N6）. Two random nucleotides were added to the 5＇ end of the selected hexamers, and 480（30 × 4~2） octamers（V8） were obtained. In general, VSITA approach showed higher enrichment of virus-targeted c DNA and enhanced ability to remove unwanted ribosomal sequences in the majorities of 45 predefined clinical samples. Moreover, VSITA combined with NGS enabled to detect not only more viruses but also achieve more viral reads hit and higher viral genome coverage in 20 clinical samples with diarrhea or fever of unknown origin. Conclusion The VSITA approach designed in this study is demonstrated to possess higher sensitivity and broader genome coverage than traditionally used random hexamers in the NGS-based identification of viral pathogens directly from clinical samples.

Microarray analysis of extracellular matrix genes expression in myocardium of mouse with Coxsackie virus B_3 myocarditis

Background Extracellular matrix (ECM) orchestrates cell behaviour including growth, death, apoptosis, adhesion, migration, and invasion by activating several signalling pathways Certain components of ECM, such as integrins, may act as receptors or co-receptors of enterovirus ECM-activated gene expressions in myocardium of viral heart disease including myocarditis and partial cardiomyopathy remain elusive This study was to investigate the expression of ECM-activated genes in myocardium of mouse with viral myocarditis Methods BALB/c mice were infected with Coxsackie virus B 3 (CVB 3) to establish an animal model of myocarditis Uninfected mice were also prepared and served as controls Specific mRNA expression pattern in myocarditic mouse heart was analysed by an in-house cDNA microarray containing 8192 genes Overexpressed ECM genes were selected and subsequently confirmed by Northern blot analysis Results Nine ECM genes were isolated, from the array of 8192 genes, as overexpressed genes in hearts of myocarditic mice in comparison with controls Subsequent Northern blot analysis confirmed that four of the nine genes were highly expressed Expression of these four genes, Fin15, ILk, Lamr1 and ADAMTS-1, has not been reported previously to be induced by Coxsackie virus Conclusion CVB 3-induced myocarditis is associated with gene expression profiles of certain ECM components

Cloning and Characterization of UL34 Gene of Pseudorabies Virus HB Isolate

In this study, China isolate HB of pseudorabies virus（PRV） was confirmed and genotypically characterized by amplifying and sequencing of partial UL34, a conservative gene involved in the egress of nucleocapsids from the nucleus, for phylogenetic analysis. The open reading frame（orf） of UL34 of PRV HB isolate is composed of 786 nucleotides, which encoded 262 amino acids. In addition, a potential transmembrane domain（241-260 aa） and 11 potential phosphorylation sites were also found in the UL34 of PRV HB isolate. Multiple amino acids alignment indicated that UL34 proteins of PRV strains derived from different geographic origins were highly conservative, but some mutations were also found. Phylogenetic analysis based on UL34 protein indicated that PRV HB strain was evolutionarily distinct from other recent China strains sequenced so far, forming a single clade within the phylogeny. Moreover, PRV HB isolate had close evolutionary relationship with Bo HV-1 and Bo HV-5 within the Alphaherpesvirinae. Taken together, these results indicated that PRV strains were in the progress of evolution. This study has expanded the knowledge of genetic profiles of PRV strains.