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?:abstract
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Background 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 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) 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 Methods 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 Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2 Results SARS-CoV-2 was identified in all except three patients 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 Besides, a very diverse group of bacterial populations were observed in the samples
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