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Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. SARS-CoV-2 was identified in all except three patients. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2.
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Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv.
#Covid 19 genome sequence analysis archive
In this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). In December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. Department of Biomedical and Diagnostic Sciences College of Veterinary Medicine, University of Tennessee, Knoxville, TN, USA DOI 10.7717/peerj.10246 Published Accepted Received Academic Editor Theerapong Krajaejun Subject Areas Microbiology, Infectious Diseases Keywords COVID-19, Influenza A virus, Human immunodeficiency virus, Co-infections, Bacteria Copyright © 2020 Abouelkhair Licence This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed.