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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Response to pegylated interferon in a COVID-19–positive elderly woman with primary myelofibrosis treated with ruxolitinib
Arthur E. Frankel,Renuka Reddy,Kayla R. DeSuza,Khaled Deeb,Aaron F. Carlin,Davey M. Smith,Yushuang Xie,Eknath Naik,Richard T. Silver,Hans Carl Hasselbalch +9 more
TL;DR: In this article, an 83-year-old female had asymptomatic SARS-CoV-2 infection while taking ruxolitinib and Pegylated interferon for 4 weeks.
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Human coronaviruses: The emergence of SARS-CoV-2 and management of COVID-19
M. Solomon,Chen Liang +1 more
TL;DR: In this article , the authors summarize the discovery and fundamental virology of HCoVs, discuss their zoonotic transmission and highlight the weak species barrier of SARS-CoV-2.
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A review of cytokine-based pathophysiology of Long COVID symptoms
Ryan J. Low,Athena Akrami +1 more
TL;DR: In this article , the authors proposed a description of the pathophysiology of the Long COVID presentation based on inflammatory cytokine cascades and the p38 MAP kinase signaling pathways that regulate cytokine production.
Journal ArticleDOI
A Short Series of Case Reports of COVID-19 in Immunocompromised Patients
Mitali Mishra,Aleena Zahra,Lokendra V. Chauhan,Riddhi Thakkar,James Ng,Shreyas Joshi,Eric D. Spitzer,Luis Marcos,W. Ian Lipkin,Nischay Mishra +9 more
TL;DR: The data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination, and may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the Sars-Cov-2 surface glycoprotein.
Journal ArticleDOI
Heterogeneity of SARS-CoV-2 virus produced in cell culture revealed by shotgun proteomics and supported by genome sequencing.
Fabrice Gallais,Olivier Pible,Jean Charles Gaillard,Stéphanie Debroas,Hélène Batina,Sylvie Ruat,Florian Sandron,Damien Delafoy,Zuzana Gerber,Robert Olaso,Fabienne Gas,Laurent Bellanger,Jean-François Deleuze,Lucia Grenga,Jean Armengaud +14 more
TL;DR: In this paper, the authors evaluated the heterogeneity of purified SARS-CoV-2 virus obtained after culturing in the Vero E6 cell line and found that cell culture induces significant changes that are translated at the protein level, such changes being detectable by tandem mass spectrometry.
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.
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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.
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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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