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.
【저자키워드】 COVID-19, influenza A virus, Co-infections, Bacteria, Human immunodeficiency virus, 【초록키워드】 coronavirus disease, SARS-CoV-2, coronavirus, Pneumonia, Human, 2019-nCoV, Infection, outcome, virus, database, Population, Adenovirus, China, infections, Host immune response, Hepatitis, outbreak, Next-generation sequencing, Wuhan, Co-infection, WHO, NL63, concern, Critical, patients, Bacterial, Emergency, World Health Organization, H7N9, acute respiratory syndrome, SARS-CoV-2 infected patients, sequence, NCBI, viral fitness, extension, métapneumovirus, PHEIC, virus genome, K -mer, Public, Sequence Read Archive, Result, caused, reported, was performed, Kraken 2, retrieved, SARS-CoV-2 infected patient, Taxonomic, 【제목키워드】 Co-infection, genome sequence, clinical sample,