26 research outputs found
A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq
BACKGROUND: Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new
approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and
veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered
during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We
describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina
MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and
circumvents both the use of PCR and the requirement for large amounts of initial template.
RESULTS: The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic
in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this
protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell
culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV)
were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads
was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates
and the type O FMDV from the serotype panel with the exception of the 5′ genomic termini and area immediately
flanking the poly(C) region.
CONCLUSIONS: We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses.
This method works successfully from a limited quantity of starting material and eliminates the requirement for
genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a
routine high-throughput diagnostic environment
Rotating Stars in Relativity
Rotating relativistic stars have been studied extensively in recent years,
both theoretically and observationally, because of the information one could
obtain about the equation of state of matter at extremely high densities and
because they are considered to be promising sources of gravitational waves. The
latest theoretical understanding of rotating stars in relativity is reviewed in
this updated article. The sections on the equilibrium properties and on the
nonaxisymmetric instabilities in f-modes and r-modes have been updated and
several new sections have been added on analytic solutions for the exterior
spacetime, rotating stars in LMXBs, rotating strange stars, and on rotating
stars in numerical relativity.Comment: 101 pages, 18 figures. The full online-readable version of this
article, including several animations, will be published in Living Reviews in
Relativity at http://www.livingreviews.org
Impact of clinical phenotypes on management and outcomes in European atrial fibrillation patients: a report from the ESC-EHRA EURObservational Research Programme in AF (EORP-AF) General Long-Term Registry
Background: Epidemiological studies in atrial fibrillation (AF) illustrate that clinical complexity increase the risk of major adverse outcomes. We aimed to describe European AF patients\u2019 clinical phenotypes and analyse the differential clinical course. Methods: We performed a hierarchical cluster analysis based on Ward\u2019s Method and Squared Euclidean Distance using 22 clinical binary variables, identifying the optimal number of clusters. We investigated differences in clinical management, use of healthcare resources and outcomes in a cohort of European AF patients from a Europe-wide observational registry. Results: A total of 9363 were available for this analysis. We identified three clusters: Cluster 1 (n = 3634; 38.8%) characterized by older patients and prevalent non-cardiac comorbidities; Cluster 2 (n = 2774; 29.6%) characterized by younger patients with low prevalence of comorbidities; Cluster 3 (n = 2955;31.6%) characterized by patients\u2019 prevalent cardiovascular risk factors/comorbidities. Over a mean follow-up of 22.5 months, Cluster 3 had the highest rate of cardiovascular events, all-cause death, and the composite outcome (combining the previous two) compared to Cluster 1 and Cluster 2 (all P <.001). An adjusted Cox regression showed that compared to Cluster 2, Cluster 3 (hazard ratio (HR) 2.87, 95% confidence interval (CI) 2.27\u20133.62; HR 3.42, 95%CI 2.72\u20134.31; HR 2.79, 95%CI 2.32\u20133.35), and Cluster 1 (HR 1.88, 95%CI 1.48\u20132.38; HR 2.50, 95%CI 1.98\u20133.15; HR 2.09, 95%CI 1.74\u20132.51) reported a higher risk for the three outcomes respectively. Conclusions: In European AF patients, three main clusters were identified, differentiated by differential presence of comorbidities. Both non-cardiac and cardiac comorbidities clusters were found to be associated with an increased risk of major adverse outcomes