Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections
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-...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2020-11-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/10246.pdf |
| _version_ | 1797418328203984896 |
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| author | Mohamed A. Abouelkhair |
| author_facet | Mohamed A. Abouelkhair |
| author_sort | Mohamed A. Abouelkhair |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:31:10Z |
| format | Article |
| id | doaj.art-8ef91d74968941f283b86c6faf25c403 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:31:10Z |
| publishDate | 2020-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-8ef91d74968941f283b86c6faf25c4032023-12-03T11:05:10ZengPeerJ Inc.PeerJ2167-83592020-11-018e1024610.7717/peerj.10246Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infectionsMohamed A. AbouelkhairBackground 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.https://peerj.com/articles/10246.pdfCOVID-19Influenza A virusHuman immunodeficiency virusCo-infectionsBacteria |
| spellingShingle | Mohamed A. Abouelkhair Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections PeerJ COVID-19 Influenza A virus Human immunodeficiency virus Co-infections Bacteria |
| title | Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections |
| title_full | Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections |
| title_fullStr | Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections |
| title_full_unstemmed | Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections |
| title_short | Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections |
| title_sort | non sars cov 2 genome sequences identified in clinical samples from covid 19 infected patients evidence for co infections |
| topic | COVID-19 Influenza A virus Human immunodeficiency virus Co-infections Bacteria |
| url | https://peerj.com/articles/10246.pdf |
| work_keys_str_mv | AT mohamedaabouelkhair nonsarscov2genomesequencesidentifiedinclinicalsamplesfromcovid19infectedpatientsevidenceforcoinfections |