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The COVID-19 pandemic has spread worldwide with alarming speed and has led to the worst healthcare crisis in a century. There was no additional external funding received for this study.Ĭompeting interests: The authors have declared that no competing interests exist.
#Covid 19 genome sequence analysis archive
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: Raw datasets are available from the NCBI Sequence Read Archive (Project ID PRJNA723604).įunding: Part of this work was supported by the National Institute of Allergy 449 and Infectious Diseases (Grant#1U19AI144297). Received: DecemAccepted: AugPublished: August 25, 2021Ĭopyright: © 2021 Doddapaneni et al. PLoS ONE 16(8):Įditor: Arnar Palsson, University of Iceland, ICELAND (2021) Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals.
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The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.Ĭitation: Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, et al. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. Analysis of junction reads revealed regions of differential transcriptional activity among samples. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames ) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19).