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
Citations
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N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains.
TL;DR: In this paper, structural and epidemiological studies of SARS-CoV-2 strain were performed to identify short and long-distance interactions that stabilize the NTD loops of the spike protein and form a critical epitope that is essential for the recognition of neutralizing antibodies from convalescent plasma.
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Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections.
TL;DR: In this article, the authors highlight the evolutionary pressures that facilitate the rise of new SARS-CoV-2 variants and the key mutations of the viral spike protein -L452R, E484K, N501Y and D614G- that promote immune escape mechanism and warrant a cautionary point for clinical and public health responses in terms of re-infection, vaccine breakthrough infection and therapeutic values.
Journal ArticleDOI
Severe impairment of T-cell responses to BNT162b2 immunization in patients with multiple myeloma
TL;DR: In this paper , the protection of the vulnerable population of patients with hematologic malignancies in the face of the ongoing COVID pandemic was discussed, and the authors suggest that some patients who fail to mount a B-cell response to vaccine may nevertheless have protective T cell responses.
Journal ArticleDOI
Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
Cathrine Scheepers,J.S. Everatt,Daniel G. Amoako,Houriiyah Tegally,Constantinos Kurt Wibmer,A. Mnguni,Arshad Ismail,B. Pinky Mahlangu,Bronwen E. Lambson,Darren P. Martin,Eduan Wilkinson,James Emmanuel San,Jennifer Giandhari,N. Manamela,Noxolo N. Ntuli,Prudence Kgagudi,Sandile Cele,Simone I. Richardson,Sureshnee Pillay,Thabo Mohale,U. Ramphal,Yeshnee Naidoo,Zamantungwa T. H. Khumalo,Gaurav Kwatra,G. Gray,Linda-Gail Bekker,Shabir A. Madhi,Vicky L. Baillie,Wesley C. Van Voorhis,Florette K. Treurnicht,Marietjie Venter,Koleka Mlisana,Nicole Wolter,Alex Sigal,Carolyn Williamson,Nei-yuan Hsiao,Nokukhanya Msomi,Tongai Maponga,Wolfgang Preiser,Zinhle Makatini,Richard J Lessells,Penny L. Moore,Tulio de Oliveira,Anne von Gottberg,Jinal N. Bhiman +44 more
TL;DR: The PANGO lineage C.1.2 was detected at low prevalence in South Africa and eleven other countries as mentioned in this paper , and was associated with a high substitution rate, and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 variants of concern or variants of interest.
Journal ArticleDOI
The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein.
Paola Cristina Resende,Felipe Gomes Naveca,Roberto D. Lins,Filipe Zimmer Dezordi,Matheus V. F. Ferraz,Matheus V. F. Ferraz,Emerson G. Moreira,Emerson G. Moreira,Danilo F. Coêlho,Danilo F. Coêlho,Fernando Couto Motta,Anna Carolina Dias Paixão,Luciana Appolinario,Renata Serrano Lopes,Ana Carolina da Fonseca Mendonça,Alice Sampaio Barreto da Rocha,Valdinete Alves do Nascimento,Victor Costa de Souza,George Silva,Fernanda Nascimento,Lidio Gonçalves Lima Neto,Fabiano Vieira da Silva,Irina Nastassja Riediger,Maria do Carmo Debur,Anderson Brandao Leite,Tirza Mattos,Cristiano Fernandes da Costa,Felicidade Mota Pereira,Cliomar Alves dos Santos,Darcita Buerger Rovaris,Sandra Fernandes,Adriano Abbud,Claudio Tavares Sacchi,Ricardo Khouri,A Bernardes,Edson Delatorre,Tiago Gräf,Marilda M. Siqueira,Gonzalo Bello,Gabriel Luz Wallau +39 more
TL;DR: In this article, the authors identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the amino (N)-terminal domain (NTD) of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region.
References
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Journal ArticleDOI
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.
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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