Explorative assessment of coronavirus-like short sequences from host-associated and environmental metagenomes

Maximilian Mora, Wisnu Adi Wicaksono, Dilfuza Egamberdieva, Robert Krause, Jose Luis Martinez, Tomislav Cernava*, Gabriele Berg*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The ongoing COVID-19 pandemic has not only globally caused a high number of causalities, but is also an unprecedented challenge for scientists. False-positive virus detection tests not only aggravate the situation in the healthcare sector, but also provide ground for speculations. Previous studies have highlighted the importance of software choice and data interpretation in virome studies. We aimed to further expand theoretical and practical knowledge in bioinformatics-driven virome studies by focusing on short, virus-like DNA sequences in metagenomic data. Analyses of datasets obtained from different sample types (terrestrial, animal and human related samples) and origins showed that coronavirus-like sequences have existed in host-associated and environmental samples before the current COVID-19 pandemic. In the analyzed datasets, various Betacoronavirus-like sequences were detected that also included SARS-CoV-2 matches. Deepening analyses indicated that the detected sequences are not of viral origin and thus should not be considered in virome profiling approaches. Our study confirms the importance of parameter selection, especially in terms of read length, for reliable virome profiling. Natural environments are an important source of coronavirus-like nucleotide sequences that should be taken into account when virome datasets are analyzed and interpreted. We therefore suggest that processing parameters are carefully selected for SARS-CoV-2 profiling in host related as well as environmental samples in order to avoid incorrect identifications.

Original languageEnglish
Article number148494
Number of pages1
JournalScience of the Total Environment
Publication statusPublished - 1 Nov 2021


  • Coronaviruses
  • COVID-19
  • Metagenomics
  • SARS-CoV-2
  • Virome profiling

ASJC Scopus subject areas

  • Pollution
  • Waste Management and Disposal
  • Environmental Engineering
  • Environmental Chemistry


  • BioTechMed-Graz

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