Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer.
Victoria A. Avanzato,Victoria A. Avanzato,M. Jeremiah Matson,M. Jeremiah Matson,Stephanie N. Seifert,Rhys Pryce,Brandi N. Williamson,Sarah L. Anzick,Kent D. Barbian,Seth D. Judson,Elizabeth R. Fischer,Craig Martens,Thomas A. Bowden,Emmie de Wit,Francis X. Riedo,Vincent J. Munster +15 more
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TLDR
The data indicate that certain immunocompromised patients may shed infectious virus for longer durations than previously recognized, and detection of subgenomic RNA is recommended in persistently SARS-CoV-2 positive individuals as a proxy for shedding of infectious virus.About:
This article is published in Cell.The article was published on 2020-12-23 and is currently open access. It has received 573 citations till now.read more
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Evaluation of a novel direct capture method for virus concentration n wastewater from COVID-19 infectious ward and correlation analysis with the number of inpatients.
TL;DR: In this article, a highly sensitive and rapid method for the virus concentration from wastewater is needed to obtain the accurate information for early detection of SARS-CoV-2 outbreak and epidemic.
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A case of multiple sclerosis with protracted course of COVID-19.
TL;DR: It is presumed that prolong high degree fever (above 38 °C) in this patient is beyond the diagnosis of post-COVID-19 syndrome and is more compatible with persistent infection.
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Evaluation of Clinical Findings and Treatment Results of Coronavirus Disease 2019 (COVID-19) in Pediatric Cancer Patients: A Single Center Experience
TL;DR: The study reveals that the mortality rate, length of hospital stay, and the need for intensive care of pediatric cancer patients with COVID-19 are higher than those of healthy children.
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Nucleocapsid antigenemia is a marker of acute SARS-CoV-2 infection
Ralf Dahrendorf,Kelly Hoogland +1 more
TL;DR: In this article , the authors proposed that viral nucleocapsid in serum or plasma may be a specific biomarker of acute infection that could enhance isolation and treatment strategies at an individualized level.
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Diagnostic Accuracy of Four Serological Tests for COVID-19 and Differences in Antibody Positivity Rates Based on the Need for Treatment or Ventilator Support
Tomonori Takano,Takashi Okanda,Masanori Hirose,Yukitaka Yamasaki,Tomoya Tsuchida,Hiromu Takemura,Kimito Kawahata,Hiroyuki Kunishima +7 more
References
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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Cutadapt removes adapter sequences from high-throughput sequencing reads
TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
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