Lack of geographical and ethnic distribution of Hepatitis B virus genotypes in Hainan Island, China.

Recent studies showed that the distribution of hepatitis B virus (HBV) genotype exhibited geographical and ethnic characteristics. Haikou city is the largest city on Hainan Island that geographically isolated from mainland of China, and is the home of multiple ethnic groups. The aim of the study was to investigate the characteristics of the HBV genotype/subgenotype distribution in Haikou city. HBV DNA was isolated from180 serum samples derived from the Han and Li groups. The HBV genotype was detected by polymerase chain reaction using genotype-specific primers and was further determined by full-length genome sequences. The results revealed that the genotype B (37.2%) and C (62.8%) were the predominant HBV genotypes in Haikou, regardless of ethnic background., Additionally, the genotype distribution was not significantly different regarding ethnicity, sex or level of serum HBV DNA. Moreover, there were multiple subgenotypes circulating in the region. In conclusion, our study revealed the diverse HBV genotypes/subgenotypes in Haikou. These findings provide a preliminary study of the distribution of HBV genotypes circulating on Hainan Island.

Complete plastome sequence of Monoon laui (Merr.) B. Xue and R.M.K. Saunders, 2012: an endemic species in Hainan.

Monoon laui (Merr.) B. Xue and R.M.K. Saunders 2012 is produced in Hainan province. The trunk is straight, the wood texture is straight, and the material is slightly soft, which is suitable for furniture and building materials. In our study, we report and characterize the complete plastome of M. laui The complete length of the plastome of M. laui possesses 161,181 bp, including a large single-copy (LSC) of 89,556 bp, small single-copy (SSC) of 18,977 bp, and two inverted repeats (IRs) of 26,313 bp. The overall G/C content in the plastome of M. laui is 39.13%. The plastome contains 257 genes, consisting of 130 protein-coding genes (16 of which are duplicated in the IR), 37 tRNA genes (seven of which are duplicated in the IR), and eight rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). Here, we explore the phylogenetic relationships and make contributions to the conservation genetics of the specie of M. laui using the complete plastome sequence.

Discrepant results of hepatitis B virus genotype determination by PCR and DNA sequencing.

Currently, multiplex-PCR with genotype-specific primers is widely used for preliminary screening of hepatitis B virus (HBV) genotypes, despite its relatively lower accuracy compared with whole genome sequencing. Here, we present the discrepant results of HBV genotyping by PCR and full-length sequencing. HBV DNA was isolated from chronic hepatitis B serum and the HBV genotype was detected by PCR using genotype-specific primers and full-length genome sequencing. As a result, the determination of genotype B by the PCR method was consistent with the DNA sequencing results; however, PCR revealed that genotype C showed a mix of B and C genotypes in the current study. In conclusion, the PCR-based genotyping may not provide accurate information of the HBV genotype and whole genome sequencing remains the "gold standard" for HBV genotyping.

Septicemic Melioidosis Detection Using Support Vector Machine with Five Immune Cell Types.

Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), predominantly occurs in the tropical regions. Of various types of melioidosis, septicemic melioidosis is the most lethal one with a mortality rate of 40%. Early detection of the disease is paramount for the better chances of cure. In this study, we developed a novel approach for septicemic melioidosis detection, using a machine learning technique-support vector machine (SVM). Several SVM models were built, and 19 features characterized by the corresponding immune cell types were generated by Cell type Identification Estimating Relative Subsets Of RNA Transcripts (CIBERSORT). Using these features, we trained a binomial SVM model on the training set and evaluated it on the independent testing set. Our findings indicated that this model performed well with means of sensitivity and specificity up to 0.962 and 0.979, respectively. Meanwhile, the receiver operating characteristic (ROC) curve analysis gave area under curves (AUCs) ranging from 0.952 to 1.000. Furthermore, we found that a concise SVM model, built upon a combination of CD8+ T cells, resting CD4+ memory T cells, monocytes, M2 macrophages, and activated mast cells, worked perfectly on the detection of septicemic melioidosis. Our data showed that its mean of sensitivity was up to 0.976 while that of specificity up to 0.993. In addition, the ROC curve analysis gave AUC close to 1.000. Taken together, this SVM model is a robust classification tool and may serve as a complementary diagnostic technique to septicemic melioidosis.

Whole Blood Transcriptome Analysis Reveals the Correlation between Specific Immune Cells and Septicemic Melioidosis.

Melioidosis is a serious infectious disease caused by the environmental Gram-negative bacillus Burkholderia pseudomallei. It has been shown that the host immune system, mainly comprising various types of immune cells, fights against the disease. The present study was to specify correlation between septicemic melioidosis and the levels of multiple immune cells. First, the genes with differential expression patterns between patients with septicemic melioidosis (B. pseudomallei) and health donors (control/healthy) were identified. These genes being related to cytokine binding, cell adhesion molecule binding, and MHC relevant proteins may influence immune response. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 23 enriched immune response pathways. We further leveraged the microarray data to investigate the relationship between immune response and septicemic melioidosis, using the CIBERSORT analysis. Comparison of the percentages of 22 immune cell types in B. pseudomallei vs. control/healthy revealed that those of CD4 memory resting cells, CD8+ T cells, B memory cells, and CD4 memory activated cells were low, whereas those of M0 macrophages, neutrophils, and gamma delta T cells were high. The multivariate logistic regression analysis further revealed that CD8+ T cells, M0 macrophages, neutrophils, and naive CD4+ cells were strongly associated with the onset of septicemic melioidosis, and M2 macrophages and neutrophils were associated with the survival in septicemic melioidosis. Taken together, these data point to a complex role of immune cells on the development and progression of melioidosis.