Abstract
BackgroundIn 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.MethodsIn 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.ResultsSARS-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.
Highlights
In December 2019, the first cases of coronavirus disease 2019 (COVID-19) were possibly due to a zoonotic transmission in China, tied to a large seafood market which traded in live wild animals [1]
We conducted identification experiments on samples sequenced from COVID-19 infected patients (Table.1)
SARS-CoV-2 was detected in all tested samples with three out of 68 clinical samples were considered negative for SARS-CoV-2 by fastv
Summary
In December 2019, the first cases of coronavirus disease 2019 (COVID-19) were possibly due to a zoonotic transmission in China, tied to a large seafood market which traded in live wild animals [1]. The causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is capable of human-to-human transmission and rapidly spread to other regions of China, and to other countries [2]. It is a global pandemic and is a considerable concern for public health. Coronaviruses in humans and animals are known to cause disease. There are three coronaviruses (severe acute respiratory syndrome coronavirus (SARS-CoV), Middle
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