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Author Spotlight: Advancements in Multiplex Detection of Respiratory Viruses
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Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for

Mohamed A Abouelkhair1

  • 1Department of Biomedical and Diagnostic Sciences College of Veterinary Medicine, University of Tennessee, Knoxville, TN, USA.

Peerj
|November 16, 2020
PubMed

Insights

This study found that patients infected with SARS-CoV-2 (the virus causing COVID-19) frequently had co-infections with other viruses and bacteria. These findings highlight the complex microbial landscape during COVID-19 infection.

Area of Science:

  • Virology
  • Microbiology
  • Genomics

Background:

  • The COVID-19 pandemic, caused by SARS-CoV-2, emerged in late 2019.
  • Co-infections significantly influence viral disease severity and host immune responses.

Purpose of the Study:

  • To investigate the presence of co-infections in patients with SARS-CoV-2.
  • To characterize the viral and bacterial communities in SARS-CoV-2 infected individuals.

Main Methods:

  • Retrieved 68 SARS-CoV-2 patient sequencing datasets from NCBI SRA.
  • Utilized alignment-free k-mer analysis (fastv) for data screening.
  • Employed Kraken 2 for taxonomic classification of non-SARS-CoV-2 sequences.

Main Results:

  • SARS-CoV-2 was detected in most patients.
  • Co-infections included influenza A (H7N9), HIV, metapneumovirus, adenovirus, herpesvirus 1, coronavirus NL63, parvovirus, SV40, and hepatitis viruses.
  • A diverse range of bacterial populations were also identified.

Conclusions:

  • SARS-CoV-2 infected patients exhibit frequent co-infections with various viruses and bacteria.
  • Understanding these co-infections is crucial for managing COVID-19 and its complications.
Abstract

Keywords:
BacteriaCOVID-19Co-infectionsHuman immunodeficiency virusInfluenza A virus

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