Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed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)

A peer-reviewed article of this Preprint also exists.

Journal reference: peerJ 2020
DOI: 10.7717/peerj.10246


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), Spodoptera frugiperda rhabdovirus isolate (3/68), Human metapneumovirus (1/68), coronaviruses NL63 (1/68), Sri Lankan cassava mosaic virus (1/68), Indian cassava mosaic virus (1/68), Parvovirus (1/68), Simian virus 40 (1/68), Woodchuck hepatitis virus (1/68), Saccharomyces 20S RNA narnavirus (2/68), and Autographa californica nucleopolyhedrovirus (2/68) genome sequences were detected in SARS-CoV-2 infected patients.


COVID-19; Viral Co-infection; SARS-CoV-2; Influenza A virus; Human Immunodeficiency virus



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