Diagnostic utility of serum bile acids in dogs presenting with epileptic seizures consistent with a tier 1 confidence level diagnosis of idiopathic epilepsy.

BACKGROUND: The International Veterinary Epilepsy Task Force consensus guidelines recommend performing fasting serum bile acid (SBA) and/or serum ammonia measurements as part of a tier 1 diagnosis of idiopathic epilepsy in dogs. The aim of this retrospective study was to determine the diagnostic utility of fasting SBA in this population. METHODS: Dogs that met the tier 1 confidence level diagnosis of idiopathic epilepsy, with the additional requirement of both fasting and 2-hour postprandial SBA measurements, were included. The incidence of significant hepatopathies and usefulness of dynamic SBA testing and minimum database results were analysed. RESULTS: A total of 233 dogs were included. All dogs diagnosed with clinically significant hepatopathy had elevations in postprandial SBA, with eight of 14 (57.14%) showing elevations in fasting SBA. The prevalence of clinically significant hepatopathies that could have been missed without using postprandial SBA measurement was 1.29%. LIMITATIONS: The further investigations performed were not uniform and there were limitations in the ability to control sampling techniques due to the retrospective nature of this study. Investigations into hepatopathy were not standardised across this study population. CONCLUSIONS: This study documents the importance of postprandial SBA measurements in the detection of hepatopathies and reveals that non-dynamic blood sampling has a negative predictive value of 91% for detecting elevated postprandial SBA, specific to dogs meeting the tier 1 confidence level diagnosis of idiopathic epilepsy.

A Novel Bead-Capture Nanopore Sequencing Method for Large Structural Rearrangement Detection in Cancer.

Rapid, cost-effective genomic stratification of structural rearrangements in cancer is often of vital importance when determining treatment; however, existing diagnostic cytogenetic and molecular testing fails to deliver the required speed when deployed at scale. Next-generation sequencing-based methods are widely used, but these can lack sensitivity and require batching of samples to be cost-effective, with long turnaround times. Here we present a novel method for rearrangement detection from genomic DNA based on third-generation long-read sequencing that overcomes these time and cost issues. The utility of this approach for the genomic stratification of patients with acute myeloid leukemia is shown based on detection of four of the most prevalent structural rearrangements. The method not only determines the precise genomic breakpoint for each expected rearrangement but also discovers and validates novel translocations in one-third of the tested samples, 80% of which involve known oncogenes. This method may prove to be a powerful tool for the diagnosis, genomic stratification, and characterization of cancers.

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission.

OBJECTIVES: To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions. METHODS: Viral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic. RESULTS: Forty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90%). Only 75/168 (45%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77%). Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50%), (b) four clusters (29%) had additional evidence of cryptic transmission, and (c) in three clusters (21%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0-2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40-50 per day) and before the impact of introducing universal face masks and banning hospital visitors. CONCLUSION: Genomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases-such as healthcare workers or asymptomatic patients-as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.

The 3.3 Å structure of a plant geminivirus using cryo-EM.

Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of Ageratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves. Our map also contains density for ~7 bases of single-stranded DNA bound to each CP, and we show that the interactions between the genome and CPs are different at the interface than in the rest of the capsid. With additional mutagenesis data, this suggests a central role for DNA binding-induced conformational change in directing the assembly of geminate capsids.