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Добірка наукової літератури з теми "SARS-CoV-2 sequencing"

Автор: Grafiati

Опубліковано: 14 березня 2023

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Статті в журналах з теми "SARS-CoV-2 sequencing"

1

Nazario-Toole, Ashley, Holly M. Nguyen, Hui Xia, Dianne N. Frankel, John W. Kieffer, and Thomas F. Gibbons. "Sequencing SARS-CoV-2 from antigen tests." PLOS ONE 17, no. 2 (2022): e0263794. http://dx.doi.org/10.1371/journal.pone.0263794.

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Анотація:

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-

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2

Mugnier, Nathalie, Aurélien Griffon, Bruno Simon, et al. "Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches." Viruses 14, no. 8 (2022): 1674. http://dx.doi.org/10.3390/v14081674.

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Анотація:

Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) to analyse SARS-CoV-2 NGS data generated on common sequencing platforms using a variety of commercially available reagents. This application performs in one click a quality check, a reference-based genome assembly, and the analysis of the generated consensus

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3

Turakhia, Yatish, Nicola De Maio, Bryan Thornlow, et al. "Stability of SARS-CoV-2 phylogenies." PLOS Genetics 16, no. 11 (2020): e1009175. http://dx.doi.org/10.1371/journal.pgen.1009175.

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The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors

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4

Sekulic, Miroslav, Holly Harper, Behtash G. Nezami, et al. "Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases." American Journal of Clinical Pathology 154, no. 2 (2020): 190–200. http://dx.doi.org/10.1093/ajcp/aqaa091.

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Abstract Objectives To report methods and findings of 2 autopsies with molecular evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals. Methods Postmortem examination was completed following Centers for Disease Control and Prevention public guidelines. Numerous formalin-fixed paraffin-embedded (FFPE) tissue types from each case were surveyed for SARS-CoV-2 RNA by quantitative reverse transcription polymerase chain reaction (qRT-PCR). SARS-CoV-2 viral genome was sequenced by next-generation sequencing (NGS) from FFPE lung tissue blocks. Results Postmort

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5

Xiaoli, Lingzi, Jill V. Hagey, Daniel J. Park, et al. "Benchmark datasets for SARS-CoV-2 surveillance bioinformatics." PeerJ 10 (September 5, 2022): e13821. http://dx.doi.org/10.7717/peerj.13821.

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Анотація:

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and check

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6

Mavzyutov, A. R., R. R. Garafutdinov, E. Yu Khalikova, et al. "The enigmas of the new coronavirus SARS-CoV-2." Biomics 13, no. 1 (2021): 75–99. http://dx.doi.org/10.31301/2221-6197.bmcs.2021-7.

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Анотація:

The emergence of the new SARS-CoV-2 coronavirus has given rise to many enigmas, to which there are no answers yet. However, the degree of threat to humanity, due to the fact that by the beginning of February 2021, more than 100 million people were ill in the world, of which 2 million died, led to the fact that the efforts of many researchers were aimed at combating this disease, including massive sequencing of the complete genomes of SARS-CoV-2, as this is necessary for diagnostics and prediction of the epidemiological situation, including in the long term. Currently, a fairly high level of co

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7

Petersen, J. M., and D. Jhala. "Sequencing for COVID-19 in the Pandemic Era: What Does it Mean?" American Journal of Clinical Pathology 156, Supplement_1 (2021): S140—S141. http://dx.doi.org/10.1093/ajcp/aqab191.300.

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Abstract Introduction/Objective SARS-CoV-2 has been developing mutations over the course of the pandemic, leading to the rise of variants. The sequencing of these variants, however, has an unclear role for the medical center providing patient treatment. Methods/Case Report Patient specimens that were positive for the presence of SARS-CoV-2 with a cycle threshold &lt;30 by reverse transcriptase polymerase chain reaction (RT-PCR) were sent for sequencing at the Veterans Health Administration Public Health Reference Laboratory (PHRL). Testing for SARS-CoV-2 was by RT-PCR was initially done by

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8

Nasir, Jalees A., Robert A. Kozak, Patryk Aftanas, et al. "A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture." Viruses 12, no. 8 (2020): 895. http://dx.doi.org/10.3390/v12080895.

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Анотація:

Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification

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9

Crawford, Dana C., and Scott M. Williams. "Global variation in sequencing impedes SARS-CoV-2 surveillance." PLOS Genetics 17, no. 7 (2021): e1009620. http://dx.doi.org/10.1371/journal.pgen.1009620.

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10

Avetyan, Diana, Siras Hakobyan, Maria Nikoghosyan, et al. "Molecular Analysis of SARS-CoV-2 Lineages in Armenia." Viruses 14, no. 5 (2022): 1074. http://dx.doi.org/10.3390/v14051074.

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Анотація:

The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase we

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