Determination of in situ detection efficiency for IM-NAA of non-standard geometrical samples

The k0-based internal mono-standard (IM) method was first proposed for the concentration analysis of samples of non-standard geometry in the 2000s. The method has demonstrated several advantages such as the elimination of gamma-ray self-attenuation and geometrical effects. On the other hand, the accuracy of the method principally depends on the in situ relative detection efficiency, which requires to be obtained in each measurement. Therefore, the relative detection efficiency is always under consideration for the improvement of the analysis results. The present paper describes a simple and automatic procedure for the determination of the relative efficiency using one or more activation products emitting gamma rays over a considered range of the spectrum. The procedure can be applied for INAA and PGNAA analysis.

Laboratory comparison of stool processing methods for Xpert® Ultra

TB disease diagnosis in children is difficult due to non-specific symptoms, paucibacillary disease and the need for invasive procedures to obtain diagnostic specimens. In many settings, these specimens are simply not collected and therefore stool, easily obtained, has emerged as a promising specimen for the diagnosis of child TB. In this study, stool from a healthy adult was spiked with known concentrations of bacille Calmette-Guérin vaccine and tested using the Xpert® Ultra assay to determine the relative detection and error rate associated with four different published stool processing methods.

A pairing of parental noroviruses with unequal competitiveness provides a clear advantage for emergence of progeny recombinants

Genetic recombination plays a pivotal role in the appearance of human norovirus recombinants that cause global epidemics. However, the factors responsible for the appearance of these recombinants remains largely unknown. In this study, we revealed a selective pressure that restricts parental combinations leading to the emergence of norovirus recombinants. To investigate traces of emerging novel recombinants and their parents in the human population, we isolated mass nucleotide sequence clones of human norovirus genogroups I and II in sewage-affected waters over a 4-year sampling period. Fourteen different phylogenetic combinations of recombinants and their parents were defined from the dozens of phylogenetic lineages circulating in the human population. To evaluate the probability of these combinations, parental lineages of each recombinant were categorized into two groups as HP (relatively higher competitive parents) and LP (relatively lower competitive parents), according to their relative detection frequency. Strong categorization of HP and LP was confirmed by tests with modified data and additional variables. An algorithm that was developed in this study to visualize the chance of mixed infection between parents revealed that HP lineages have a higher chance of mixed infection than LP lineages in the human population. Three parental pairing types in recombinants were defined: HP-HP, HP-LP, and LP-LP. Among these, most recombinants were identified as HP-LP, despite the prediction of dominant emergence of HP-HP type recombinants. These results suggest that nature favors recombinants of human norovirus that originate from parental pairing of heterogeneous competitiveness. IMPORTANCE Novel recombinants, generated from inter- and intra-species recombination of norovirus lineages, often emerge and pose a threat to public health. However, the factors determining emergence of these particular recombinants from all possible combinations of parental lineages remains largely unknown. Therefore, current investigations on these recombinants are inevitably limited to post-epidemic analyses, which merely identify genetic or phenotypic changes in the newly emerged recombinants compared to their parents. Here, we have provided a new theoretical concept that emergence of novel recombinants could be explained by a combination of parental noroviruses thriving in the human population and those circulating at lower levels. This study could provide additional and important rationale for the proactive environmental monitoring of potential future epidemics due to viral recombinants.

Inferring identical by descent sharing of sample ancestors promotes high resolution relative detection

As genetic datasets increase in size, the fraction of samples with one or more close relatives grows rapidly, resulting in sets of mutually related individuals. We present DRUID—Deep Relatedness Utilizing Identity by Descent—a method that works by inferring the identical by descent (IBD) sharing profile of an ungenotyped ancestor of a set of close relatives. Using this IBD profile, DRUID infers relatedness between unobserved ancestors and more distant relatives, thereby combining information from multiple samples to remove one or more generations between the deep relationships to be identified. DRUID constructs sets of close relatives by detecting full siblings and also uses a novel approach to identify the aunts/uncles of two or more siblings, recovering 92.2% of real aunts/uncles with zero false positives. In real and simulated data, DRUID correctly infers up to 10.5% more relatives than PADRE when using data from two sets of distantly related siblings, and 10.7–31.3% more relatives given two sets of siblings and their aunts/uncles. DRUID frequently infers relationships either correctly or within one degree of the truth, with PADRE classifying 43.3–58.3% of tenth degree relatives in this way compared to 79.6–96.7% using DRUID.