PreprintArticleVersion 2Preserved in Portico This version is not peer-reviewed
Non-coronavirus Genome Sequences Identified from Metagenomic Analysis of Clinical Samples from COVID-19 Infected Patients: An Evidence for Co-infection
Version 1
: Received: 31 May 2020 / Approved: 31 May 2020 / Online: 31 May 2020 (20:36:28 CEST)
Version 2
: Received: 17 June 2020 / Approved: 18 June 2020 / Online: 18 June 2020 (04:57:14 CEST)
Abouelkhair, M. A. Non-SARS-CoV-2 Genome Sequences Identified in Clinical Samples from COVID-19 Infected Patients: Evidence for Co-Infections. PeerJ, 2020, 8, e10246. https://doi.org/10.7717/peerj.10246.
Abouelkhair, M. A. Non-SARS-CoV-2 Genome Sequences Identified in Clinical Samples from COVID-19 Infected Patients: Evidence for Co-Infections. PeerJ, 2020, 8, e10246. https://doi.org/10.7717/peerj.10246.
Abouelkhair, M. A. Non-SARS-CoV-2 Genome Sequences Identified in Clinical Samples from COVID-19 Infected Patients: Evidence for Co-Infections. PeerJ, 2020, 8, e10246. https://doi.org/10.7717/peerj.10246.
Abouelkhair, M. A. Non-SARS-CoV-2 Genome Sequences Identified in Clinical Samples from COVID-19 Infected Patients: Evidence for Co-Infections. PeerJ, 2020, 8, e10246. https://doi.org/10.7717/peerj.10246.
Abstract
In December 2019, pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection emerged in Wuhan City, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused epidemic disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be the sixth international public health emergency. Cellular co-infection is a critical determinant of both viral fitness and infection outcome and plays a crucial role in shaping the host immune response to infections. In this study, sixty-eight public next-generation sequencing libraries from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Using an alignment-free method based on K-mer mapping and extension, SARS-CoV-2 was identified in all except three patients. Influenza A H7N9 (3/68), Human immunodeficiency virus 1 (1/68), rhabdovirus isolate (3/68), Human metapneumovirus (1/68), coronaviruses NL63 (1/68), Parvovirus (1/68), Simian virus 40 (1/68), and hepatitis virus (1/68) genome sequences were detected in SARS-CoV-2 infected patients.
Keywords
COVID-19; Viral Co-infection; SARS-CoV-2; Influenza A virus; Human Immunodeficiency virus
Subject
Biology and Life Sciences, Virology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Commenter: Mohamed Abouelkhair
Commenter's Conflict of Interests: Author