The development of a beacon-based real-time PCR for cytomegalovirus and its application in immunocompromised patients.

BACKGROUND: Because of the high cost of commercially available quantitative PCR kits, we developed a beacon- based real-time PCR (B-rt-PCR) for Cytomegalovirus (CMV) viral load determination. METHODS: A total of 197 samples from 60 immunocompromised patients, who were bone marrow transplantation recipients or had hematological malignancies, were tested using B-rt-PCR, COBAS Amplicor CMV Monitor test (Amplicor CMV test), and conventional CMV PCR. The correlation results among these 3 assays were calculated. RESULTS: In these 197 samples, the CMV viral load determined by B-rt-PCR for positive specimens ranged from 19.8 to 4148.7 copies/10(5) peripheral blood mononuclear cells (PBMCs). When any positive result of B-rt-PCR, the Amplicor CMV test, or conventional PCR was considered as "CMV positive" for the 56 specimens tested by all three methods, we found that the positive and negative predictive values, respectively, were 100% and 98.6% for B-rt-PCR, 100% and 46.2% for the Amplicor CMV test, and 100% and 89.4% for conventional PCR. These three methods had good specificity (all 100%). However, the sensitivity rate of B-rt-PCR (96.3%) was higher compared to the Amplicor CMV test (46.2%) and conventional PCR (89.4%). CONCLUSIONS: The B-rt-PCR is evaluated to be a sensitive method for CMV detection in immunocompromised patients.

Topographic influence on ecohydrology in volcanic watersheds of the western Pacific monsoon area: evidence from water stable isotope composition of meteoric water, thermal water, and plants.

In Taiwanese volcanic watersheds, we investigated stable water isotopes in meteoric water, plants, and thermal water. Meteoric water exhibited a seasonal cycle, with heavier isotopes in winter and lighter ones in summer, especially in the southern region. The northern monsoon signal lagged the south by two weeks. In the Tatun mountains, young water fractions indicated prevalent old water sources. In the northern watershed, streamwater mainly came from the winter monsoon, while the southern one was influenced by alternating monsoons. Both indices indicated that winter plants depended on summer rainfall. Streamwater and plants had distinct sources in winter, supporting ecohydrological separation. Thermal spring water's d-excess helped identify water-rock interactions, with low d value signaling such interactions. The topographic wetness index showed a higher summer monsoon contribution to southern streamwater but a lower one to plants. The mean linear channel direction significantly affected the monsoon contribution fraction, with northeast-oriented channels vulnerable to northeastward winter monsoons. Finally, we developed a model illustrating hydrological processes on short and long timescales. Our findings enhance our understanding of hydrological disturbances' impact on water resources and ecosystems.

Evolutionary histories of coxsackievirus B5 and swine vesicular disease virus reconstructed by phylodynamic and sequence variation analyses.

Coxsackievirus (CV)-B5 is a common human enterovirus reported worldwide; swine vesicular disease virus (SVDV) is a porcine variant of CV-B5. To clarify the transmission dynamics and molecular basis of host switching between CV-B5 and SVDV, we analysed and compared the VP1 and partial 3Dpol gene regions of these two viruses. Spatiotemporal dynamics of viral transmission were estimated using a Bayesian statistical inference framework. The detected selection events were used to analyse the key molecules associated with host switching. Analyses of VP1 sequences revealed six CV-B5 genotypes (A1-A4 and B1-B2) and three SVDV genotypes (I-III). Analyses of partial 3Dpol revealed five clusters (A-E). The genotypes evolved sequentially over different periods, albeit with some overlap. The major hub of CV-B5 transmission was in China whereas the major hubs of SVDV transmission were in Italy. Network analysis based on deduced amino acid sequences showed a diverse extension of the VP1 structural protein, whereas most sequences were clustered into two haplotypes in the partial 3Dpol region. Residue 178 of VP1 showed four epistatic interactions with residues known to play essential roles in viral host tropism, cell entry, and viral decoating.