CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance.

SUMMARY: The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast. AVAILABILITY AND IMPLEMENTATION: CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MRI-Based Quantitation of Hepatic Steatosis Does Not Predict Hypertrophy Rate after Portal Vein Embolization in Patients with Colorectal Liver Metastasis and Normal to Moderately Elevated Fat Fraction.

The aim of this study was to correlate the pre-procedural magnetic-resonance-imaging-based hepatic fat fraction (hFF) with the degree of hypertrophy after portal vein embolization (PVE) in patients with colorectal cancer liver metastases (CRCLM). Between 2011 November and 2020 February, 68 patients with CRCLM underwent magnetic resonance imaging (MRI; 1.5 Tesla) of the liver before PVE. Using T1w chemical shift imaging (DUAL FFE), the patients were categorized as having a normal (<5%) or an elevated (>5%) hFF. The correlation of hFF, age, gender, initial tumor mass, history of chemotherapy, degree of liver hypertrophy, and kinetic growth rate after PVE was investigated using multiple regression analysis and Spearman's test. A normal hFF was found in 43/68 patients (63%), whereas 25/68 (37%) patients had an elevated hFF. The mean hypertrophy and kinetic growth rates in patients with normal vs. elevated hFF were 24 ± 31% vs. 28 ± 36% and 9 ± 9 % vs. 8 ± 10% (p > 0.05), respectively. Spearman's test showed no correlation between hFF and the degree of hypertrophy (R = -0.04). Multivariable analysis showed no correlation between hFF, history of chemotherapy, age, baseline tumor burden, or laterality of primary colorectal cancer, and only a poor inverse correlation between age and kinetic growth rate after PVE. An elevated hFF in a pre-procedural MRI does not correlate with the hypertrophy rate after PVE and should therefore not be used as a contraindication to the procedure in patients with CRCLM.

Induction of Contralateral Hepatic Hypertrophy by Unilobar Yttrium-90 Transarterial Radioembolization versus Portal Vein Embolization: An Animal Study.

PURPOSE: To compare hepatic hypertrophy in the contralateral lobe achieved by unilobar transarterial radioembolization (TARE) versus portal vein embolization (PVE) in a swine model. METHODS: After an escalation study to determine the optimum dose to achieve hypertrophy after unilobar TARE in 4 animals, 16 pigs were treated by TARE (yttrium-90 resin microspheres) or PVE (lipiodol/n-butyl cyanoacrylate). Liver volume was calculated based on CT before treatment and during 6 months of follow-up. Independent t-test (P < .05) was used to compare hypertrophy. The relationship between hypertrophy after TARE and absorbed dose was calculated using the Pearson correlation. RESULTS: At 2 and 4 weeks after treatment, a significantly higher degree of future liver remnant hypertrophy was observed in the PVE group versus the TARE group, with a median volume gain of 31% (interquartile range [IQR]: 16%-66%) for PVE versus 23% (IQR: 6%-36%) for TARE after 2 weeks and 51% (IQR: 47%-69%) for PVE versus 29% (IQR: 20%-50%) for TARE after 4 weeks. After 3 and 6 months, hypertrophy converged without a statistically significant difference, with a volume gain of 103% (IQR: 86%-119%) for PVE versus 82% (IQR: 70%-96%) for TARE after 3 months and 115% (IQR: 70%-46%) for PVE versus 86% (IQR: 58%-111%) for TARE after 6 months. A strong correlation was observed between radiation dose (median 162 Gy, IQR: 139-175) and hypertrophy. CONCLUSIONS: PVE resulted in rapid hypertrophy within 1 month of the procedure, followed by a plateau, whereas TARE resulted in comparable hypertrophy by 3-6 months. TARE-induced hypertrophy correlated with radiation absorbed dose.

Retrograde Recanalization of the Celiac Artery via the Pancreaticoduodenal Arcade as a Safe and Valid Alternative to Antegrade Access.

PURPOSE: The antegrade recanalization of an occlusion or high-grade stenosis of the celiac artery via the aorta often represents a technical challenge. A retrograde approach via the superior mesenteric artery and the pancreaticoduodenal arcade may be an alternative approach. Based on our experience, we assess the technical success and the short- and mid-term outcomes of this bailout procedure. METHODS: We performed a retrospective analysis of all consecutive patients who underwent recanalization and stent implantation in the celiac artery between January 2010 and December 2018. Data on vascular access, the materials used including stents, as well as the length of the intervention, radiation exposure, and follow-up were assessed. RESULTS: Recanalization in combination with stent implantation into the celiac artery was performed in 43 patients. In 39 (91%) of 43 patients, the recanalization was successful with an antegrade approach via the aorta, whereas in 4 (9%) of 43 patients the passage of the stenosis was possible only through a retrograde approach through the superior mesenteric artery and the pancreaticoduodenal arcade followed be advancement of the microwire through the celiac artery into the aorta. The tip of the microwire was captured in the aorta with a snare and pulled out in the femoral introducer sheath and used as a guide for the antegrade implantation of a balloon-expandable stent. CONCLUSIONS: The retrograde recanalization of the celiac artery via the pancreaticoduodenal arcade may be technically challenging yet represents a feasible alternative in case of a failed antegrade approach.