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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Correlation between Type I Interferon Associated Factors and COVID-19 Severity
TL;DR: The role and dysregulation of plasmacytoid dendritic cells (pDCs) and type I interferons (IFN) axis in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discussed in this paper .
Journal ArticleDOI
Occurrence and transport of SARS-CoV-2 in wastewater streams and its detection and remediation by chemical-biological methods
TL;DR: In this article , the authors highlighted several methods of collection, sampling and monitoring/estimation as well as surveillance tool for detecting SARS-CoV in wastewater streams and found that WBE (Wastewater based epidemiology) is the most effective surveillance tool.
Journal ArticleDOI
SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis
Richard Lueking,Andrew E. Clark,Madhusudhanan Narasimhan,Lenin Mahimainathan,Alagarraju Muthukumar,Christian P. Larsen,Jeffrey A. Soller +6 more
TL;DR: Five COVID-19 cases caused by coinfection with different SARS-CoV-2 variants (Delta/Omicron BA.1 and OmicronBA.2) as identified by multiplex fragment analysis are described.
Posted ContentDOI
A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus.
Klaudia Chrzastek,Chandana Tennakoon,Dagmara Bialy,Graham L Freimanis,John Flannery,Holly Shelton +5 more
TL;DR: In this article, the SISPA method was used for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples.
Journal ArticleDOI
Prolonged SARS-CoV-2 Infection With Common Features in Two Patients Receiving Anti-CD20 Therapy
Amalia Papanikolopoulou,Vasilis Thimis,Eirini Antonogiannaki,Vasiliki Rapti,Konstantinos Tsiakos,Giannis Krallis,Sofia Ntouraki,G Kokkotis,Emmanouil Panagiotou,Vissaria Sakka,E. Kakalou,Thomas Nitsotolis,Garyphallia Poulakou,Konstantinos N. Syrigos +13 more
TL;DR: In this paper , the authors describe two cases of prolonged SARS-CoV-2 infection with common features, in two patients receiving anti-CD20 therapies, the first for chronic lymphocytic leukemia (CLL) and the second for rheumatoid arthritis (RA).
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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